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Liu P, Panda K, Edwards SA, Swanson R, Yi H, Pandesha P, Hung YH, Klaas G, Ye X, Collins MV, Renken KN, Gilbertson LA, Veena V, Hancock CN, Slotkin RK. Transposase-assisted target-site integration for efficient plant genome engineering. Nature 2024; 631:593-600. [PMID: 38926583 PMCID: PMC11254759 DOI: 10.1038/s41586-024-07613-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/28/2024] [Indexed: 06/28/2024]
Abstract
The current technologies to place new DNA into specific locations in plant genomes are low frequency and error-prone, and this inefficiency hampers genome-editing approaches to develop improved crops1,2. Often considered to be genome 'parasites', transposable elements (TEs) evolved to insert their DNA seamlessly into genomes3-5. Eukaryotic TEs select their site of insertion based on preferences for chromatin contexts, which differ for each TE type6-9. Here we developed a genome engineering tool that controls the TE insertion site and cargo delivered, taking advantage of the natural ability of the TE to precisely excise and insert into the genome. Inspired by CRISPR-associated transposases that target transposition in a programmable manner in bacteria10-12, we fused the rice Pong transposase protein to the Cas9 or Cas12a programmable nucleases. We demonstrated sequence-specific targeted insertion (guided by the CRISPR gRNA) of enhancer elements, an open reading frame and a gene expression cassette into the genome of the model plant Arabidopsis. We then translated this system into soybean-a major global crop in need of targeted insertion technology. We have engineered a TE 'parasite' into a usable and accessible toolkit that enables the sequence-specific targeting of custom DNA into plant genomes.
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Affiliation(s)
- Peng Liu
- Donald Danforth Plant Science Center, St Louis, MO, USA
| | - Kaushik Panda
- Donald Danforth Plant Science Center, St Louis, MO, USA
| | - Seth A Edwards
- Donald Danforth Plant Science Center, St Louis, MO, USA
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Ryan Swanson
- Donald Danforth Plant Science Center, St Louis, MO, USA
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Hochul Yi
- Plant Transformation Facility, Donald Danforth Plant Science Center, St Louis, MO, USA
| | - Pratheek Pandesha
- Donald Danforth Plant Science Center, St Louis, MO, USA
- Division of Biology and Biomedical Sciences, Washington University, St Louis, MO, USA
| | - Yu-Hung Hung
- Donald Danforth Plant Science Center, St Louis, MO, USA
| | - Gerald Klaas
- Donald Danforth Plant Science Center, St Louis, MO, USA
| | - Xudong Ye
- Bayer Crop Science, St Louis, MO, USA
| | | | | | | | - Veena Veena
- Plant Transformation Facility, Donald Danforth Plant Science Center, St Louis, MO, USA
| | | | - R Keith Slotkin
- Donald Danforth Plant Science Center, St Louis, MO, USA.
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA.
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2
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Hancock CN, Germany T, Redd P, Timmons J, Lipford J, Burns S, Cervantes-Perez SA, Libault M, Shen W, An YQC, Kanizay L, Yerka M, Parrott WA. Identification and characterization of a temperature sensitive chlorotic soybean mutant. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.02.578604. [PMID: 38352530 PMCID: PMC10862810 DOI: 10.1101/2024.02.02.578604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Screening a transposon-mutagenized soybean population led to the discovery of a recessively inherited chlorotic phenotype. This "vir1" phenotype results in smaller stature, weaker stems, and a smaller root system with smaller nodules. Genome sequencing identified 15 candidate genes with mutations likely to result in a loss of function. Amplicon sequencing of a segregating population was then used to narrow the list to a single candidate mutation, a single-base change in Glyma.07G102300 that disrupts splicing of the second intron. Single cell transcriptomic profiling indicates that this gene is expressed primarily in mesophyll cells and RNA sequencing data indicates it is upregulated in germinating seedlings by cold stress. Previous studies have shown that mutations to Os05g34040, the rice homolog of Glyma.07G102300, produced a chlorotic phenotype that was more pronounced in cool temperatures. Growing soybean vir1 mutants at lower temperatures also resulted in a more severe phenotype. In addition, transgenic expression of wild type Glyma.07G102300 in the knockout mutant of the Arabidopsis homolog At4930720 rescues the chlorotic phenotype, further supporting the hypothesis that the mutation in Glyma.07G102300 is causal of the vir1 phenotype.
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Affiliation(s)
- C. Nathan Hancock
- Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC
| | | | - Priscilla Redd
- Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC
| | - Jack Timmons
- Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC
| | - Jeffery Lipford
- Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC
| | - Samantha Burns
- Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC
| | | | - Marc Libault
- Plant Science and Technology, University of Missouri, Columbia, MO
| | - Wenhao Shen
- Donald Danforth Plant Science Center, St. Louis, MO
| | - Yong-qiang Charles An
- USDA-ARS Plant Genetics Research Unit, Danforth Plant Science Center, Saint Louis, MO
| | - Lisa Kanizay
- Center for Applied Genetic Technology, University of Georgia, Athens, GA
| | - Melinda Yerka
- Center for Applied Genetic Technology, University of Georgia, Athens, GA
- Department of Agriculture, Veterinary and Rangeland Sciences, University of Nevada, Reno, NV
| | - Wayne A. Parrott
- Center for Applied Genetic Technology, University of Georgia, Athens, GA
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3
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Redd PS, Payero L, Gilbert DM, Page CA, King R, McAssey EV, Bodie D, Diaz S, Hancock CN. Transposase expression, element abundance, element size, and DNA repair determine the mobility and heritability of PIF/ Pong/ Harbinger transposable elements. Front Cell Dev Biol 2023; 11:1184046. [PMID: 37363729 PMCID: PMC10288884 DOI: 10.3389/fcell.2023.1184046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/22/2023] [Indexed: 06/28/2023] Open
Abstract
Introduction: Class II DNA transposable elements account for significant portions of eukaryotic genomes and contribute to genome evolution through their mobilization. To escape inactivating mutations and persist in the host genome over evolutionary time, these elements must be mobilized enough to result in additional copies. These elements utilize a "cut and paste" transposition mechanism that does not intrinsically include replication. However, elements such as the rice derived mPing element have been observed to increase in copy number over time. Methods: We used yeast transposition assays to test several parameters that could affect the excision and insertion of mPing and its related elements. This included development of novel strategies for measuring element insertion and sequencing insertion sites. Results: Increased transposase protein expression increased the mobilization frequency of a small (430 bp) element, while overexpression inhibition was observed for a larger (7,126 bp) element. Smaller element size increased both the frequency of excision and insertion of these elements. The effect of yeast ploidy on element excision, insertion, and copy number provided evidence that homology dependent repair allows for replicative transposition. These elements were found to preferentially insert into yeast rDNA repeat sequences. Discussion: Identifying the parameters that influence transposition of these elements will facilitate their use for gene discovery and genome editing. These insights in to the behavior of these elements also provide important clues into how class II transposable elements have shaped eukaryotic genomes.
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Affiliation(s)
- Priscilla S. Redd
- Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC, United States
| | - Lisette Payero
- Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC, United States
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
| | - David M. Gilbert
- Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC, United States
| | - Clinton A. Page
- Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC, United States
| | - Reese King
- Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC, United States
| | - Edward V. McAssey
- Department of Crop and Soil Science, Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Athens, GA, United States
| | - Dalton Bodie
- Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC, United States
| | - Stephanie Diaz
- Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC, United States
| | - C. Nathan Hancock
- Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC, United States
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4
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Development of Ethyl Methanesulfonate Mutant Edamame Soybean (Glycine max (L.) Merr.) Populations and Forward and Reverse Genetic Screening for Early-Flowering Mutants. PLANTS 2022; 11:plants11141839. [PMID: 35890474 PMCID: PMC9315854 DOI: 10.3390/plants11141839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/10/2022] [Accepted: 07/11/2022] [Indexed: 11/26/2022]
Abstract
Induced mutation is a viable breeding strategy that is widely utilized in the development of elite plant varieties. We aimed to improve a variety of edamame by constructing novel mutant populations using the ethyl methanesulfonate in soybeans (Glycine max (L.) Merr.). In the M2 population, the flowering stage showed a considerable standard deviation compared to the wild type, confirming that the mutant populations had the expected DNA mutations. To identify the DNA mutations in the mutant populations, we used the targeting induced local lesions in genomes (TILLING) method, which is a reverse genetic method, to search for soybean flowering-related gene mutants. A total of 30 mutants from E1, E3, E4, and PhyA1 genes, which are known to be highly effective genes, or their homologous gene for flowering and maturation found in soybean quantitative trait locus analyses were isolated from our TILLING screening. Among these mutants, there were eleven nonsynonymous substitution mutants, one nonsense mutant, and two single nucleotide deletion mutants that could be expected to reduce or eliminate gene function. The e1, e3, and e4 mutants obtained in this study flowered considerably earlier than the wild type. In particular, the e1 mutant with a nonsynonymous substitution flowered approximately 1 month after sowing regardless of the sowing date, and its harvest date was approximately 1 month earlier than that of the wild type. Mutations identified using the TILLING method could not only be used as gel-based DNA markers with the same manipulation method, but the mutations could also be detected as DNA markers by the high-resolution melting method. These results indicate that mutations achieved without chromosome modification by crossbreeding are effective for early and practical improvement of superior varieties and that efficient selection of mutants by reverse genetics is an effective method for the identification of genetic modifications. The edamame mutant populations developed in this study are believed to possess various useful alleles which may be applicable in the search for mutations that lead to improved edamame yield and eating quality beyond the flowering stage.
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5
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Helliwell EE, Lafayette P, Kronmiller BN, Arredondo F, Duquette M, Co A, Vega-Arreguin J, Porter SS, Borrego EJ, Kolomiets MV, Parrott WA, Tyler BM. Transgenic Soybeans Expressing Phosphatidylinositol-3-Phosphate-Binding Proteins Show Enhanced Resistance Against the Oomycete Pathogen Phytophthora sojae. Front Microbiol 2022; 13:923281. [PMID: 35783378 PMCID: PMC9243418 DOI: 10.3389/fmicb.2022.923281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
Oomycete and fungal pathogens cause billions of dollars of damage to crops worldwide annually. Therefore, there remains a need for broad-spectrum resistance genes, especially ones that target pathogens but do not interfere with colonization by beneficial microbes. Motivated by evidence suggesting that phosphatidylinositol-3-phosphate (PI3P) may be involved in the delivery of some oomycete and fungal virulence effector proteins, we created stable transgenic soybean plants that express and secrete two different PI3P-binding proteins, GmPH1 and VAM7, in an effort to interfere with effector delivery and confer resistance. Soybean plants expressing the two PI3P-binding proteins exhibited reduced infection by the oomycete pathogen Phytophthora sojae compared to control lines. Measurements of nodulation by nitrogen-fixing mutualistic bacterium Bradyrhizobium japonicum, which does not produce PI3P, revealed that the two lines with the highest levels of GmPH1 transcripts exhibited reductions in nodulation and in benefits from nodulation. Transcriptome and plant hormone measurements were made of soybean lines with the highest transcript levels of GmPH1 and VAM7, as well as controls, following P. sojae- or mock-inoculation. The results revealed increased levels of infection-associated transcripts in the transgenic lines, compared to controls, even prior to P. sojae infection, suggesting that the plants were primed for increased defense. The lines with reduced nodulation exhibited elevated levels of jasmonate-isoleucine and of transcripts of a JAR1 ortholog encoding jasmonate-isoleucine synthetase. However, lines expressing VAM7 transgenes exhibited normal nodulation and no increases in jasmonate-isoleucine. Overall, together with previously published data from cacao and from P. sojae transformants, the data suggest that secretion of PI3P-binding proteins may confer disease resistance through a variety of mechanisms.
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Affiliation(s)
- Emily E. Helliwell
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
- School of Biological Sciences, Washington State University, Vancouver, WA, United States
- *Correspondence: Emily E. Helliwell,
| | - Peter Lafayette
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
| | - Brent N. Kronmiller
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Felipe Arredondo
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Madeleine Duquette
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Anna Co
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Julio Vega-Arreguin
- Escuela Nacional de Estudios Superiores – León, Universidad Nacional Autónoma de México, León, Mexico
| | - Stephanie S. Porter
- School of Biological Sciences, Washington State University, Vancouver, WA, United States
| | - Eli J. Borrego
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, United States
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Michael V. Kolomiets
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, United States
| | - Wayne A. Parrott
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
| | - Brett M. Tyler
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
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6
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Zhou X, He J, Velanis CN, Zhu Y, He Y, Tang K, Zhu M, Graser L, de Leau E, Wang X, Zhang L, Andy Tao W, Goodrich J, Zhu JK, Zhang CJ. A domesticated Harbinger transposase forms a complex with HDA6 and promotes histone H3 deacetylation at genes but not TEs in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1462-1474. [PMID: 33960113 DOI: 10.1111/jipb.13108] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 05/01/2021] [Indexed: 06/12/2023]
Abstract
In eukaryotes, histone acetylation is a major modification on histone N-terminal tails that is tightly connected to transcriptional activation. HDA6 is a histone deacetylase involved in the transcriptional regulation of genes and transposable elements (TEs) in Arabidopsis thaliana. HDA6 has been shown to participate in several complexes in plants, including a conserved SIN3 complex. Here, we uncover a novel protein complex containing HDA6, several Harbinger transposon-derived proteins (HHP1, SANT1, SANT2, SANT3, and SANT4), and MBD domain-containing proteins (MBD1, MBD2, and MBD4). We show that mutations of all four SANT genes in the sant-null mutant cause increased expression of the flowering repressors FLC, MAF4, and MAF5, resulting in a late flowering phenotype. Transcriptome deep sequencing reveals that while the SANT proteins and HDA6 regulate the expression of largely overlapping sets of genes, TE silencing is unaffected in sant-null mutants. Our global histone H3 acetylation profiling shows that SANT proteins and HDA6 modulate gene expression through deacetylation. Collectively, our findings suggest that Harbinger transposon-derived SANT domain-containing proteins are required for histone deacetylation and flowering time control in plants.
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Affiliation(s)
- Xishi Zhou
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Junna He
- College of Horticulture, China Agricultural University, Beijing, 100193, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette,, IN 47907, USA
| | - Christos N Velanis
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Daniel Rutherford Building, Max Born Crescent, Edinburgh, EH9 3BF, United Kingdom
| | - Yiwang Zhu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Yuhan He
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Kai Tang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette,, IN 47907, USA
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Mingku Zhu
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette,, IN 47907, USA
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Lisa Graser
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Daniel Rutherford Building, Max Born Crescent, Edinburgh, EH9 3BF, United Kingdom
- University of Applied Sciences Mannheim, Paul-Wittsack-Str. 10,, Mannheim, 68163, Germany
| | - Erica de Leau
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Daniel Rutherford Building, Max Born Crescent, Edinburgh, EH9 3BF, United Kingdom
| | - Xingang Wang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette,, IN 47907, USA
| | - Lingrui Zhang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette,, IN 47907, USA
| | - W Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette,, IN 47907, USA
| | - Justin Goodrich
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Daniel Rutherford Building, Max Born Crescent, Edinburgh, EH9 3BF, United Kingdom
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Cui-Jun Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
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7
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Yadav N, Narang J, Chhillar AK, Rana JS. CRISPR: A new paradigm of theranostics. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2021; 33:102350. [PMID: 33359413 PMCID: PMC7831819 DOI: 10.1016/j.nano.2020.102350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/09/2020] [Accepted: 12/15/2020] [Indexed: 12/26/2022]
Abstract
Infectious and hereditary diseases are the primary cause of human mortality globally. Applications of conventional techniques require significant improvement in sensitivity and specificity in therapeutics. However, clustered regularly interspaced short palindromic repeats (CRISPRs) is an innovative genome editing technology which has provided a significant therapeutic tool exhibiting high sensitivity, fast and precise investigation of distinct pathogens in an epidemic. CRISPR technology has also facilitated the understanding of the biology and therapeutic mechanism of cancer and several other hereditary diseases. Researchers have used the CRISPR technology as a theranostic approach for a wide range of diseases causing pathogens including distinct bacteria, viruses, fungi and parasites and genetic mutations as well. In this review article, besides various therapeutic applications of infectious and hereditary diseases we have also explained the structure and mechanism of CRISPR tools and role of CRISPR integrated biosensing technology in provoking diagnostic applications.
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Affiliation(s)
- Neelam Yadav
- Department of Biotechnology, Deenbandhu Chhotu Ram University of Science and Technology, Murthal, Sonepat; Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana.
| | - Jagriti Narang
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, Hamdard Nagar, New Delhi, India.
| | | | - Jogender Singh Rana
- Department of Biotechnology, Deenbandhu Chhotu Ram University of Science and Technology, Murthal, Sonepat.
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Torabi S, Sukumaran A, Dhaubhadel S, Johnson SE, LaFayette P, Parrott WA, Rajcan I, Eskandari M. Effects of type I Diacylglycerol O-acyltransferase (DGAT1) genes on soybean (Glycine max L.) seed composition. Sci Rep 2021; 11:2556. [PMID: 33510334 PMCID: PMC7844222 DOI: 10.1038/s41598-021-82131-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 01/15/2021] [Indexed: 01/30/2023] Open
Abstract
Type I Diacylglycerol acyltransferase (DGAT1) catalyzes the final step of the biosynthesis process of triacylglycerol (TAG), the major storage lipids in plant seeds, through the esterification of diacylglycerol (DAG). To characterize the function of DGAT1 genes on the accumulation of oil and other seed composition traits in soybean, transgenic lines were generated via trans-acting siRNA technology, in which three DGAT1 genes (Glyma.13G106100, Glyma.09G065300, and Glyma.17G053300) were downregulated. The simultaneous downregulation of the three isoforms in transgenic lines was found to be associated with the reduction of seed oil concentrations by up to 18 mg/g (8.3%), which was correlated with increases in seed protein concentration up to 42 mg/g (11%). Additionally, the downregulations also influenced the fatty acid compositions in the seeds of transgenic lines through increasing the level of oleic acid, up to 121 mg/g (47.3%). The results of this study illustrate the importance of DGAT1 genes in determining the seed compositions in soybean through the development of new potential technology for manipulating seed quality in soybean to meet the demands for its various food and industrial applications.
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Affiliation(s)
- Sepideh Torabi
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Arjun Sukumaran
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Sangeeta Dhaubhadel
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Sarah E Johnson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Peter LaFayette
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Wayne A Parrott
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, USA
| | - Istvan Rajcan
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Milad Eskandari
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada.
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9
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Johnson A, Mcassey E, Diaz S, Reagin J, Redd PS, Parrilla DR, Nguyen H, Stec A, McDaniel LAL, Clemente TE, Stupar RM, Parrott WA, Hancock CN. Development of mPing-based activation tags for crop insertional mutagenesis. PLANT DIRECT 2021; 5:e00300. [PMID: 33506165 PMCID: PMC7814626 DOI: 10.1002/pld3.300] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 11/13/2020] [Accepted: 12/07/2020] [Indexed: 06/12/2023]
Abstract
Modern plant breeding increasingly relies on genomic information to guide crop improvement. Although some genes are characterized, additional tools are needed to effectively identify and characterize genes associated with crop traits. To address this need, the mPing element from rice was modified to serve as an activation tag to induce expression of nearby genes. Embedding promoter sequences in mPing resulted in a decrease in overall transposition rate; however, this effect was negated by using a hyperactive version of mPing called mmPing20. Transgenic soybean events carrying mPing-based activation tags and the appropriate transposase expression cassettes showed evidence of transposition. Expression analysis of a line that contained a heritable insertion of the mmPing20F activation tag indicated that the activation tag induced overexpression of the nearby soybean genes. This represents a significant advance in gene discovery technology as activation tags have the potential to induce more phenotypes than the original mPing element, improving the overall effectiveness of the mutagenesis system.
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Affiliation(s)
- Alexander Johnson
- Institute of Plant Breeding, Genetics & Genomics/Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensGAUSA
| | - Edward Mcassey
- Institute of Plant Breeding, Genetics & Genomics/Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensGAUSA
- Present address:
School of Life SciencesUniversity of Hawaiʻi at MānoaHonoluluHIUSA
| | - Stephanie Diaz
- Department of Biology and GeologyUniversity of South Carolina AikenAikenSCUSA
- Present address:
Department of BiochemistryPurdue UniversityWest LafayetteINUSA
| | - Jacob Reagin
- Department of Biology and GeologyUniversity of South Carolina AikenAikenSCUSA
| | - Priscilla S. Redd
- Department of Biology and GeologyUniversity of South Carolina AikenAikenSCUSA
| | - Daymond R. Parrilla
- Department of Biology and GeologyUniversity of South Carolina AikenAikenSCUSA
- Present address:
Department of Molecular and Comparative PathobiologyJohns Hopkins School of MedicineBaltimoreMDUSA
| | - Hanh Nguyen
- Department of Agronomy and Horticulture/Center for Plant Science InnovationUniversity of NebraskaLincolnNEUSA
| | - Adrian Stec
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMNUSA
| | - Lauren A. L. McDaniel
- Institute of Plant Breeding, Genetics & Genomics/Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensGAUSA
| | - Thomas E. Clemente
- Department of Agronomy and Horticulture/Center for Plant Science InnovationUniversity of NebraskaLincolnNEUSA
| | - Robert M. Stupar
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMNUSA
| | - Wayne A. Parrott
- Institute of Plant Breeding, Genetics & Genomics/Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensGAUSA
| | - C. Nathan Hancock
- Department of Biology and GeologyUniversity of South Carolina AikenAikenSCUSA
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10
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Genomic diversity generated by a transposable element burst in a rice recombinant inbred population. Proc Natl Acad Sci U S A 2020; 117:26288-26297. [PMID: 33020276 PMCID: PMC7584900 DOI: 10.1073/pnas.2015736117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Genomes of all characterized higher eukaryotes harbor examples of transposable element (TE) bursts-the rapid amplification of TE copies throughout a genome. Despite their prevalence, understanding how bursts diversify genomes requires the characterization of actively transposing TEs before insertion sites and structural rearrangements have been obscured by selection acting over evolutionary time. In this study, rice recombinant inbred lines (RILs), generated by crossing a bursting accession and the reference Nipponbare accession, were exploited to characterize the spread of the very active Ping/mPing family through a small population and the resulting impact on genome diversity. Comparative sequence analysis of 272 individuals led to the identification of over 14,000 new insertions of the mPing miniature inverted-repeat transposable element (MITE), with no evidence for silencing of the transposase-encoding Ping element. In addition to new insertions, Ping-encoded transposase was found to preferentially catalyze the excision of mPing loci tightly linked to a second mPing insertion. Similarly, structural variations, including deletion of rice exons or regulatory regions, were enriched for those with break points at one or both ends of linked mPing elements. Taken together, these results indicate that structural variations are generated during a TE burst as transposase catalyzes both the high copy numbers needed to distribute linked elements throughout the genome and the DNA cuts at the TE ends known to dramatically increase the frequency of recombination.
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11
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Velanis CN, Perera P, Thomson B, de Leau E, Liang SC, Hartwig B, Förderer A, Thornton H, Arede P, Chen J, Webb KM, Gümüs S, De Jaeger G, Page CA, Hancock CN, Spanos C, Rappsilber J, Voigt P, Turck F, Wellmer F, Goodrich J. The domesticated transposase ALP2 mediates formation of a novel Polycomb protein complex by direct interaction with MSI1, a core subunit of Polycomb Repressive Complex 2 (PRC2). PLoS Genet 2020; 16:e1008681. [PMID: 32463832 PMCID: PMC7282668 DOI: 10.1371/journal.pgen.1008681] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 06/09/2020] [Accepted: 02/18/2020] [Indexed: 12/17/2022] Open
Abstract
A large fraction of plant genomes is composed of transposable elements (TE), which provide a potential source of novel genes through “domestication”–the process whereby the proteins encoded by TE diverge in sequence, lose their ability to catalyse transposition and instead acquire novel functions for their hosts. In Arabidopsis, ANTAGONIST OF LIKE HETEROCHROMATIN PROTEIN 1 (ALP1) arose by domestication of the nuclease component of Harbinger class TE and acquired a new function as a component of POLYCOMB REPRESSIVE COMPLEX 2 (PRC2), a histone H3K27me3 methyltransferase involved in regulation of host genes and in some cases TE. It was not clear how ALP1 associated with PRC2, nor what the functional consequence was. Here, we identify ALP2 genetically as a suppressor of Polycomb-group (PcG) mutant phenotypes and show that it arose from the second, DNA binding component of Harbinger transposases. Molecular analysis of PcG compromised backgrounds reveals that ALP genes oppose silencing and H3K27me3 deposition at key PcG target genes. Proteomic analysis reveals that ALP1 and ALP2 are components of a variant PRC2 complex that contains the four core components but lacks plant-specific accessory components such as the H3K27me3 reader LIKE HETEROCHROMATION PROTEIN 1 (LHP1). We show that the N-terminus of ALP2 interacts directly with ALP1, whereas the C-terminus of ALP2 interacts with MULTICOPY SUPPRESSOR OF IRA1 (MSI1), a core component of PRC2. Proteomic analysis reveals that in alp2 mutant backgrounds ALP1 protein no longer associates with PRC2, consistent with a role for ALP2 in recruitment of ALP1. We suggest that the propensity of Harbinger TE to insert in gene-rich regions of the genome, together with the modular two component nature of their transposases, has predisposed them for domestication and incorporation into chromatin modifying complexes. A large part of the genomes of plants and animals consists of transposable elements (TE), which are usually considered as selfish or parasitic as they encode proteins (transposases) which promote TE proliferation but not functions useful for their hosts. As a result, hosts have evolved ways of reducing TE proliferation, usually by modifying the DNA or chromatin of TE so that their transposases are no longer produced. Once the TE are inactivated they can no longer proliferate and over time they accumulate mutations and can evolve new functions, often beneficial for their hosts. This process is known as domestication and is increasingly recognised as a potent source of evolutionary novelty. For example, the CRISPR/Cas system that has provided the basis for a revolution in genetic engineering (“genome editing”) has evolved via domestication of transposons in bacteria. We have identified the ALP proteins, two domesticated transposases which function as components of an enzyme complex (PRC2) involved in modifying chromatin and regulating host gene activity in plants. Here we show how ALPs contact PRC2 and direct formation of a novel complex that lacks several of the usual components. The ALPs and related proteins will provide valuable tools for manipulating plant chromatin.
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Affiliation(s)
- Christos N. Velanis
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Daniel Rutherford Building, Max Born Crescent, Edinburgh, United Kingdom
| | - Pumi Perera
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Daniel Rutherford Building, Max Born Crescent, Edinburgh, United Kingdom
| | - Bennett Thomson
- Smurfit Institute of Genetics, Trinity College Dublin, Ireland
| | - Erica de Leau
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Daniel Rutherford Building, Max Born Crescent, Edinburgh, United Kingdom
| | - Shih Chieh Liang
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Daniel Rutherford Building, Max Born Crescent, Edinburgh, United Kingdom
| | - Ben Hartwig
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Alexander Förderer
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Harry Thornton
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Daniel Rutherford Building, Max Born Crescent, Edinburgh, United Kingdom
| | - Pedro Arede
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Daniel Rutherford Building, Max Born Crescent, Edinburgh, United Kingdom
| | - Jiawen Chen
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Daniel Rutherford Building, Max Born Crescent, Edinburgh, United Kingdom
| | - Kimberly M. Webb
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, United Kingdom
| | - Serin Gümüs
- Department of Biotechnology, Mannheim University of Applied Science, Mannheim, Germany
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- VIB Center for Plant Systems Biology, Gent, Belgium
| | - Clinton A. Page
- Department of Biology & Geology, University of South Carolina Aiken, Aiken, South Carolina, United States of America
| | - C. Nathan Hancock
- Department of Biology & Geology, University of South Carolina Aiken, Aiken, South Carolina, United States of America
| | - Christos Spanos
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, United Kingdom
| | - Juri Rappsilber
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, United Kingdom
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Philipp Voigt
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, United Kingdom
| | - Franziska Turck
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Frank Wellmer
- Smurfit Institute of Genetics, Trinity College Dublin, Ireland
| | - Justin Goodrich
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Daniel Rutherford Building, Max Born Crescent, Edinburgh, United Kingdom
- * E-mail:
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12
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Campbell BW, Hoyle JW, Bucciarelli B, Stec AO, Samac DA, Parrott WA, Stupar RM. Functional analysis and development of a CRISPR/Cas9 allelic series for a CPR5 ortholog necessary for proper growth of soybean trichomes. Sci Rep 2019; 9:14757. [PMID: 31611562 PMCID: PMC6791840 DOI: 10.1038/s41598-019-51240-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 09/27/2019] [Indexed: 11/19/2022] Open
Abstract
Developments in genomic and genome editing technologies have facilitated the mapping, cloning, and validation of genetic variants underlying trait variation. This study combined bulked-segregant analysis, array comparative genomic hybridization, and CRISPR/Cas9 methodologies to identify a CPR5 ortholog essential for proper trichome growth in soybean (Glycine max). A fast neutron mutant line exhibited short trichomes with smaller trichome nuclei compared to its parent line. A fast neutron-induced deletion was identified within an interval on chromosome 6 that co-segregated with the trichome phenotype. The deletion encompassed six gene models including an ortholog of Arabidopsis thaliana CPR5. CRISPR/Cas9 was used to mutate the CPR5 ortholog, resulting in five plants harboring a total of four different putative knockout alleles and two in-frame alleles. Phenotypic analysis of the mutants validated the candidate gene, and included intermediate phenotypes that co-segregated with the in-frame alleles. These findings demonstrate that the CPR5 ortholog is essential for proper growth and development of soybean trichomes, similar to observations in A. thaliana. Furthermore, this work demonstrates the value of using CRISPR/Cas9 to generate an allelic series and intermediate phenotypes for functional analysis of candidate genes and/or the development of novel traits.
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Affiliation(s)
- Benjamin W Campbell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA.
| | - Jacob W Hoyle
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, USA
| | - Bruna Bucciarelli
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA
- USDA-ARS-Plant Science Research Unit, St. Paul, MN, USA
| | - Adrian O Stec
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA
| | - Deborah A Samac
- USDA-ARS-Plant Science Research Unit, St. Paul, MN, USA
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
| | - Wayne A Parrott
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, USA
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA.
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Insertional Mutagenesis Approaches and Their Use in Rice for Functional Genomics. PLANTS 2019; 8:plants8090310. [PMID: 31470516 PMCID: PMC6783850 DOI: 10.3390/plants8090310] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 08/07/2019] [Accepted: 08/07/2019] [Indexed: 01/01/2023]
Abstract
Insertional mutagenesis is an indispensable tool for engendering a mutant population using exogenous DNA as the mutagen. The advancement in the next-generation sequencing platform has allowed for faster screening and analysis of generated mutated populations. Rice is a major staple crop for more than half of the world's population; however, the functions of most of the genes in its genome are yet to be analyzed. Various mutant populations represent extremely valuable resources in order to achieve this goal. Here, we have reviewed different insertional mutagenesis approaches that have been used in rice, and have discussed their principles, strengths, and limitations. Comparisons between transfer DNA (T-DNA), transposons, and entrapment tagging approaches have highlighted their utilization in functional genomics studies in rice. We have also summarised different forward and reverse genetics approaches used for screening of insertional mutant populations. Furthermore, we have compiled information from several efforts made using insertional mutagenesis approaches in rice. The information presented here would serve as a database for rice insertional mutagenesis populations. We have also included various examples which illustrate how these populations have been useful for rice functional genomics studies. The information provided here will be very helpful for future functional genomics studies in rice aimed at its genetic improvement.
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14
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Krishnamurthy P, Fujisawa Y, Takahashi Y, Abe H, Yamane K, Mukaiyama K, Son HR, Hiraga S, Kaga A, Anai T, Tsukamoto C, Ishimoto M. High-Throughput Screening and Characterization of a High-Density Soybean Mutant Library Elucidate the Biosynthesis Pathway of Triterpenoid Saponins. PLANT & CELL PHYSIOLOGY 2019; 60:1082-1097. [PMID: 30753604 DOI: 10.1093/pcp/pcz025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 01/31/2019] [Indexed: 05/21/2023]
Abstract
Triterpenes (C30) constitute one of the diverse class of natural products with potential applications in food, cosmetic and pharmaceutical industries. Soyasaponins are oleanane-type triterpenoids widespread among legumes and particularly abundant in soybean seeds. They have associated with various pharmacological implications and undesirable taste properties of soybean-based food products. Uncovering the biosynthetic genes of soyasaponins will provide new opportunities to control the pathway for human benefits. However, the pathway of soyasaponin biosynthesis has not been fully elucidated in part because of a paucity of natural mutants. Here, we applied a structured high-density soybean mutant library for the forward genetic screening of triterpenoid biosynthesis. The seed soyasaponin polymorphism in the mutant library was evaluated using a high-throughput thin-layer chromatography and liquid chromatography tandem mass spectrometry analysis. This screening identified 35 mutants (3.85% of 909 mutant lines) with seven unusual soyasaponin phenotypes (Categories 1-7), which was greater than the number of natural mutants reported previously (22 mutants, 0.18% of ∼12,428 accessions). Nine unique intermediates of soyasaponin biosynthesis were identified and their chemical structures were estimated based on their MS/MS fragment patterns. Based on published information, 19 mutants could be associated with loss of function of four individual soyasaponin biosynthesis genes identified through expressed sequence tag mining or positional cloning, whereas the remaining 16 mutants were novel and may facilitate discovery of the unknown biosynthetic genes of soyasaponins. Our approach and library may help to identify new phenotype materials and causative genes associated with specialized metabolite production and other traits.
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Affiliation(s)
| | | | - Yuya Takahashi
- Faculty of Agriculture, Iwate University, Morioka, Iwate, Japan
| | - Hanako Abe
- Faculty of Agriculture, Iwate University, Morioka, Iwate, Japan
| | - Kentaro Yamane
- Faculty of Agriculture, Iwate University, Morioka, Iwate, Japan
| | | | - Hae-Reon Son
- Faculty of Agriculture, Iwate University, Morioka, Iwate, Japan
| | - Susumu Hiraga
- Institute of Crop Science, NARO, Tsukuba, Ibaraki, Japan
| | - Akito Kaga
- Institute of Crop Science, NARO, Tsukuba, Ibaraki, Japan
| | - Toyoaki Anai
- Faculty of Agriculture, Saga University, Saga, Japan
| | | | - Masao Ishimoto
- Institute of Crop Science, NARO, Tsukuba, Ibaraki, Japan
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15
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Mikuriya S, Kasai M, Nakashima K, Natasia, Hase Y, Yamada T, Abe J, Kanazawa A. Frequent generation of mutants with coincidental changes in multiple traits via ion-beam irradiation in soybean. Genes Genet Syst 2018; 92:153-161. [PMID: 28674272 DOI: 10.1266/ggs.16-00034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Ion beams are powerful mutagens that can induce novel mutants in plants. We previously established a system for producing a mutant population of soybean via ion-beam irradiation, isolated plants that had chlorophyll deficiency, and maintained their progeny via self-fertilization. Here we report the characterization of the progeny plants in terms of chlorophyll content, flowering time and isoflavone content in seeds. Chlorophyll deficiency in the leaf tissues was linked with reduced levels of isoflavones, the major flavonoid compounds accumulated in soybean seeds, which suggested the involvement of metabolic changes associated with the chlorophyll deficiency. Intriguingly, flowering time was frequently altered in plants that had a reduced level of chlorophyll in the leaf tissues. Plant lines that flowered either earlier or later than the wild-type plants were detected. The observed coincidental changes were presumed to be attributable to the following origins: structural changes of DNA segments leading to the loss of multiple gene functions, or indirect effects of mutations that affect one of these traits, which were manifested as phenotypic changes in the background of the duplicated composition of the soybean genome.
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Affiliation(s)
- Shun Mikuriya
- Research Faculty of Agriculture, Hokkaido University
| | - Megumi Kasai
- Research Faculty of Agriculture, Hokkaido University
| | | | - Natasia
- Research Faculty of Agriculture, Hokkaido University
| | - Yoshihiro Hase
- Takasaki Advanced Radiation Research Institute, National Institutes for Quantum and Radiological Science and Technology
| | | | - Jun Abe
- Research Faculty of Agriculture, Hokkaido University
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16
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Espina MJ, Ahmed CMS, Bernardini A, Adeleke E, Yadegari Z, Arelli P, Pantalone V, Taheri A. Development and Phenotypic Screening of an Ethyl Methane Sulfonate Mutant Population in Soybean. FRONTIERS IN PLANT SCIENCE 2018; 9:394. [PMID: 29651295 PMCID: PMC5884938 DOI: 10.3389/fpls.2018.00394] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 03/12/2018] [Indexed: 05/04/2023]
Abstract
Soybean is an important oil-producing crop in the Fabaceae family and there are increasing demands for soybean oil and other soybean products. Genetic improvement of soybean is needed to increase its production. In order to provide genetic diversity and resources for identifying important genes, a new ethyl methane sulfonate (EMS) mutagenized soybean population was generated using the newly released germplasm, JTN-5203 (maturity group V). Treatment of soybean seeds with 60 mM EMS concentration was found to be suitable for inducing mutation. A total of 1,820 M1 individuals were produced from 15,000 treated seeds. The resulting M2 population was planted in the field for phenotyping. After harvest, seed traits including total oil, protein, starch, moisture content, fatty acid and amino acid compositions were measured by NIR. Phenotypic variations observed in this population include changes in leaf morphology, plant architecture, seed compositions, and yield. Of most interest, we identified plants with increased amounts of total protein (50% vs. 41% for control) and plants with higher amounts of total oil (25% vs. 21.2% control). Similarly, we identified plants with increases in oleic acid content and decreases in linoleic acid and linolenic acid. This EMS mutant population will be used for further studies including screening for various traits such as amino acid pathways, allergens, phytic acids, and other important soybean agronomic traits. In addition, these mutant individuals will be evaluated in the next generation to assess the heritability. Beneficial traits from these mutants can be exploited for future soybean breeding programs. This germplasm can also be used for discovering novel mutant alleles and for functional gene expression analysis using reverse genetics tools such as TILLING.
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Affiliation(s)
- Mary J. Espina
- Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN, United States
| | - C. M. Sabbir Ahmed
- Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN, United States
| | - Angelina Bernardini
- Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN, United States
| | - Ekundayo Adeleke
- Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN, United States
| | - Zeinab Yadegari
- Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN, United States
| | - Prakash Arelli
- United States Department of Agriculture, Agricultural Research Service, Jackson, TN, United States
| | - Vince Pantalone
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
| | - Ali Taheri
- Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN, United States
- *Correspondence: Ali Taheri,
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17
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Tracking the genome-wide outcomes of a transposable element burst over decades of amplification. Proc Natl Acad Sci U S A 2017; 114:E10550-E10559. [PMID: 29158416 PMCID: PMC5724284 DOI: 10.1073/pnas.1716459114] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Rice (Oryza sativa) has a unique combination of attributes that made it an ideal host to track the natural behavior of very active transposable elements (TEs) over generations. In this study, we have exploited its small genome and propagation by self or sibling pollination to identify and characterize two strain pairs, EG4/HEG4 and A119/A123, undergoing bursts of the nonautonomous miniature inverted repeat transposable element mPing. Comparative sequence analyses of these strains have advanced our understanding of (i) factors that contribute to sustaining a TE burst for decades, (ii) features that distinguish a natural TE burst from bursts in cell culture or mutant backgrounds, and (iii) the extent to which TEs can rapidly diversify the genome of an inbred organism. To understand the success strategies of transposable elements (TEs) that attain high copy numbers, we analyzed two pairs of rice (Oryza sativa) strains, EG4/HEG4 and A119/A123, undergoing decades of rapid amplification (bursts) of the class 2 autonomous Ping element and the nonautonomous miniature inverted repeat transposable element (MITE) mPing. Comparative analyses of whole-genome sequences of the two strain pairs validated that each pair has been maintained for decades as inbreds since divergence from their respective last common ancestor. Strains EG4 and HEG4 differ by fewer than 160 SNPs and a total of 264 new mPing insertions. Similarly, strains A119 and A123 exhibited about half as many SNPs (277) as new mPing insertions (518). Examination of all other potentially active TEs in these genomes revealed only a single new insertion out of ∼40,000 loci surveyed. The virtual absence of any new TE insertions in these strains outside the mPing bursts demonstrates that the Ping/mPing family gradually attains high copy numbers by maintaining activity and evading host detection for dozens of generations. Evasion is possible because host recognition of mPing sequences appears to have no impact on initiation or maintenance of the burst. Ping is actively transcribed, and both Ping and mPing can transpose despite methylation of terminal sequences. This finding suggests that an important feature of MITE success is that host recognition does not lead to the silencing of the source of transposase.
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18
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Kandoth PK, Liu S, Prenger E, Ludwig A, Lakhssassi N, Heinz R, Zhou Z, Howland A, Gunther J, Eidson S, Dhroso A, LaFayette P, Tucker D, Johnson S, Anderson J, Alaswad A, Cianzio SR, Parrott WA, Korkin D, Meksem K, Mitchum MG. Systematic Mutagenesis of Serine Hydroxymethyltransferase Reveals an Essential Role in Nematode Resistance. PLANT PHYSIOLOGY 2017; 175:1370-1380. [PMID: 28912378 PMCID: PMC5664460 DOI: 10.1104/pp.17.00553] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 09/11/2017] [Indexed: 05/27/2023]
Abstract
Rhg4 is a major genetic locus that contributes to soybean cyst nematode (SCN) resistance in the Peking-type resistance of soybean (Glycine max), which also requires the rhg1 gene. By map-based cloning and functional genomic approaches, we previously showed that the Rhg4 gene encodes a predicted cytosolic serine hydroxymethyltransferase (GmSHMT08); however, the novel gain of function of GmSHMT08 in SCN resistance remains to be characterized. Using a forward genetic screen, we identified an allelic series of GmSHMT08 mutants that shed new light on the mechanistic aspects of GmSHMT08-mediated resistance. The new mutants provide compelling genetic evidence that Peking-type rhg1 resistance in cv Forrest is fully dependent on the GmSHMT08 gene and demonstrates that this resistance is mechanistically different from the PI 88788-type of resistance that only requires rhg1 We also demonstrated that rhg1-a from cv Forrest, although required, does not exert selection pressure on the nematode to shift from HG type 7, which further validates the bigenic nature of this resistance. Mapping of the identified mutations onto the SHMT structural model uncovered key residues for structural stability, ligand binding, enzyme activity, and protein interactions, suggesting that GmSHMT08 has additional functions aside from its main enzymatic role in SCN resistance. Lastly, we demonstrate the functionality of the GmSHMT08 SCN resistance gene in a transgenic soybean plant.
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Affiliation(s)
- Pramod K Kandoth
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211
| | - Shiming Liu
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, Illinois 62901
| | - Elizabeth Prenger
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211
| | - Andrew Ludwig
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211
| | - Naoufal Lakhssassi
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, Illinois 62901
| | - Robert Heinz
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211
| | - Zhou Zhou
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, Illinois 62901
| | - Amanda Howland
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211
| | - Joshua Gunther
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, Illinois 62901
| | - Samantha Eidson
- Mathematics and Computer Science Department, Fontbonne University, St. Louis, Missouri 63105
| | - Andi Dhroso
- Department of Computer Science and Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, Massachusetts 01609
| | - Peter LaFayette
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602
| | - Donna Tucker
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602
| | - Sarah Johnson
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602
| | - James Anderson
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, Illinois 62901
| | - Alaa Alaswad
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, Illinois 62901
| | | | - Wayne A Parrott
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602
| | - Dmitry Korkin
- Department of Computer Science and Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, Massachusetts 01609
| | - Khalid Meksem
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, Illinois 62901
| | - Melissa G Mitchum
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211
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19
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Modulating signaling networks by CRISPR/Cas9-mediated transposable element insertion. Curr Genet 2017; 64:405-412. [DOI: 10.1007/s00294-017-0765-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 10/01/2017] [Accepted: 10/09/2017] [Indexed: 12/11/2022]
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20
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Patil G, Mian R, Vuong T, Pantalone V, Song Q, Chen P, Shannon GJ, Carter TC, Nguyen HT. Molecular mapping and genomics of soybean seed protein: a review and perspective for the future. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1975-1991. [PMID: 28801731 PMCID: PMC5606949 DOI: 10.1007/s00122-017-2955-8] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/26/2017] [Indexed: 05/16/2023]
Abstract
KEY MESSAGE Genetic improvement of soybean protein meal is a complex process because of negative correlation with oil, yield, and temperature. This review describes the progress in mapping and genomics, identifies knowledge gaps, and highlights the need of integrated approaches. Meal protein derived from soybean [Glycine max (L) Merr.] seed is the primary source of protein in poultry and livestock feed. Protein is a key factor that determines the nutritional and economical value of soybean. Genetic improvement of soybean seed protein content is highly desirable, and major quantitative trait loci (QTL) for soybean protein have been detected and repeatedly mapped on chromosomes (Chr.) 20 (LG-I), and 15 (LG-E). However, practical breeding progress is challenging because of seed protein content's negative genetic correlation with seed yield, other seed components such as oil and sucrose, and interaction with environmental effects such as temperature during seed development. In this review, we discuss rate-limiting factors related to soybean protein content and nutritional quality, and potential control factors regulating seed storage protein. In addition, we describe advances in next-generation sequencing technologies for precise detection of natural variants and their integration with conventional and high-throughput genotyping technologies. A syntenic analysis of QTL on Chr. 15 and 20 was performed. Finally, we discuss comprehensive approaches for integrating protein and amino acid QTL, genome-wide association studies, whole-genome resequencing, and transcriptome data to accelerate identification of genomic hot spots for allele introgression and soybean meal protein improvement.
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Affiliation(s)
- Gunvant Patil
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Rouf Mian
- Soybean and Nitrogen Fixation Unit, USDA-ARS, Raleigh, NC, 27607, USA.
| | - Tri Vuong
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Vince Pantalone
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996-4561, USA
| | - Qijian Song
- Agricultural Research Service, Department of Agriculture United States, Beltsville, MD, 20705, USA
| | - Pengyin Chen
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Grover J Shannon
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Tommy C Carter
- Soybean and Nitrogen Fixation Unit, USDA-ARS, Raleigh, NC, 27607, USA
| | - Henry T Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA.
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21
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Sandhu D, Ghosh J, Johnson C, Baumbach J, Baumert E, Cina T, Grant D, Palmer RG, Bhattacharyya MK. The endogenous transposable element Tgm9 is suitable for generating knockout mutants for functional analyses of soybean genes and genetic improvement in soybean. PLoS One 2017; 12:e0180732. [PMID: 28797084 PMCID: PMC5552171 DOI: 10.1371/journal.pone.0180732] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 06/20/2017] [Indexed: 11/19/2022] Open
Abstract
In soybean, variegated flowers can be caused by somatic excision of the CACTA-type transposable element Tgm9 from Intron 2 of the DFR2 gene encoding dihydroflavonol-4-reductase of the anthocyanin pigment biosynthetic pathway. DFR2 was mapped to the W4 locus, where the allele containing Tgm9 was termed w4-m. In this study we have demonstrated that previously identified morphological mutants (three chlorophyll deficient mutants, one male sterile-female fertile mutant, and three partial female sterile mutants) were caused by insertion of Tgm9 following its excision from DFR2. Analyses of Tgm9 insertion sites among 105 independent mutants demonstrated that Tgm9 hops to all 20 soybean chromosomes from its original location on Chromosome 17. Some genomic regions are prone to increased Tgm9-insertions. Tgm9 transposed over 25% of the time into exon or intron sequences. Tgm9 is therefore suitable for generating an indexed insertional mutant collection for functional analyses of most soybean genes. Furthermore, desirable Tgm9-induced stable knockout mutants can be utilized in generating improved traits for commercial soybean cultivars.
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Affiliation(s)
- Devinder Sandhu
- USDA-ARS, US Salinity Laboratory, Riverside, CA, United States of America
| | - Jayadri Ghosh
- Department of Agronomy, Iowa State University, Ames, IA, United States of America
| | - Callie Johnson
- Department of Biology, University of Wisconsin-Stevens Point, Stevens Point, WI, United States of America
| | - Jordan Baumbach
- Department of Agronomy, Iowa State University, Ames, IA, United States of America
| | - Eric Baumert
- Department of Biology, University of Wisconsin-Stevens Point, Stevens Point, WI, United States of America
| | - Tyler Cina
- Department of Biology, University of Wisconsin-Stevens Point, Stevens Point, WI, United States of America
| | - David Grant
- Department of Agronomy, Iowa State University, Ames, IA, United States of America
- USDA-ARS Corn Insects and Crop Genomics Research Unit, Ames, IA, United States of America
| | - Reid G. Palmer
- Department of Agronomy, Iowa State University, Ames, IA, United States of America
- USDA-ARS Corn Insects and Crop Genomics Research Unit, Ames, IA, United States of America
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22
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Guo C, Spinelli M, Ye C, Li QQ, Liang C. Genome-Wide Comparative Analysis of Miniature Inverted Repeat Transposable Elements in 19 Arabidopsis thaliana Ecotype Accessions. Sci Rep 2017; 7:2634. [PMID: 28572566 PMCID: PMC5454002 DOI: 10.1038/s41598-017-02855-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 04/20/2017] [Indexed: 01/03/2023] Open
Abstract
Miniature inverted repeat transposable elements (MITEs) are prevalent in eukaryotic genomes. They are known to critically influence the process of genome evolution and play a role in gene regulation. As the first study concentrated in the transposition activities of MITEs among different ecotype accessions within a species, we conducted a genome-wide comparative analysis by characterizing and comparing MITEs in 19 Arabidopsis thaliana accessions. A total of 343485 MITE putative sequences, including canonical, diverse and partial ones, were delineated from all 19 accessions. Within the entire population of MITEs sequences, 80.7% of them were previously unclassified MITEs, demonstrating a different genomic distribution and functionality compared to the classified MITEs. The interactions between MITEs and homologous genes across 19 accessions provided a fine source for analyzing MITE transposition activities and their impacts on genome evolution. Moreover, a significant proportion of MITEs were found located in the last exon of genes besides the ordinary intron locality, thus potentially modifying the end of genes. Finally, analysis of the impact of MITEs on gene expression suggests that migrations of MITEs have no detectable effect on the expression level for host genes across accessions.
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Affiliation(s)
- Cheng Guo
- Department of Biology, Miami University, Oxford, OH, 45056, USA
| | | | - Congting Ye
- Key Laboratory of the Ministry of Education for Costal and Wetland Ecosystems College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Qingshun Q Li
- Key Laboratory of the Ministry of Education for Costal and Wetland Ecosystems College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China.
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, 91766, USA.
| | - Chun Liang
- Department of Biology, Miami University, Oxford, OH, 45056, USA.
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23
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Sedivy EJ, Wu F, Hanzawa Y. Soybean domestication: the origin, genetic architecture and molecular bases. THE NEW PHYTOLOGIST 2017; 214:539-553. [PMID: 28134435 DOI: 10.1111/nph.14418] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 11/28/2016] [Indexed: 05/20/2023]
Abstract
Domestication provides an important model for the study of evolution, and information learned from domestication research aids in the continued improvement of crop species. Recent progress in de novo assembly and whole-genome resequencing of wild and cultivated soybean genomes, in addition to new archeological discoveries, sheds light on the origin of this important crop and provides a clearer view on the modes of artificial selection that drove soybean domestication and diversification. This novel genomic information enables the search for polymorphisms that underlie variation in agronomic traits and highlights genes that exhibit a signature of selection, leading to the identification of a number of candidate genes that may have played important roles in soybean domestication, diversification and improvement. These discoveries provide a novel point of comparison on the evolutionary bases of important agronomic traits among different crop species.
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Affiliation(s)
- Eric J Sedivy
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Faqiang Wu
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yoshie Hanzawa
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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24
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Han MJ, Zhou QZ, Zhang HH, Tong X, Lu C, Zhang Z, Dai F. iMITEdb: the genome-wide landscape of miniature inverted-repeat transposable elements in insects. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw148. [PMID: 28025339 PMCID: PMC5199201 DOI: 10.1093/database/baw148] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 09/19/2016] [Accepted: 10/18/2016] [Indexed: 01/23/2023]
Abstract
Miniature inverted-repeat transposable elements (MITEs) have attracted much attention due to their widespread occurrence and high copy numbers in eukaryotic genomes. However, the systematic knowledge about MITEs in insects and other animals is still lacking. In this study, we identified 6012 MITE families from 98 insect species genomes. Comparison of these MITEs with known MITEs in the NCBI non-redundant database and Repbase showed that 5701(∼95%) of 6012 MITE families are novel. The abundance of MITEs varies drastically among different insect species, and significantly correlates with genome size. In general, larger genomes contain more MITEs than small genomes. Furthermore, all identified MITEs were included in a newly constructed database (iMITEdb) (http://gene.cqu.edu.cn/iMITEdb/), which has functions such as browse, search, BLAST and download. Overall, our results not only provide insight on insect MITEs but will also improve assembly and annotation of insect genomes. More importantly, the results presented in this study will promote studies of MITEs function, evolution and application in insects. Database URL: http://gene.cqu.edu.cn/iMITEdb/
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Affiliation(s)
- Min-Jin Han
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing 400715, China
| | - Qiu-Zhong Zhou
- Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Hua-Hao Zhang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang 332000, China
| | - Xiaoling Tong
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing 400715, China
| | - Cheng Lu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing 400715, China
| | - Ze Zhang
- Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Fangyin Dai
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing 400715, China
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25
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Campbell BW, Hofstad AN, Sreekanta S, Fu F, Kono TJY, O'Rourke JA, Vance CP, Muehlbauer GJ, Stupar RM. Fast neutron-induced structural rearrangements at a soybean NAP1 locus result in gnarled trichomes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:1725-38. [PMID: 27282876 PMCID: PMC4983299 DOI: 10.1007/s00122-016-2735-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/28/2016] [Indexed: 05/20/2023]
Abstract
KEY MESSAGE Three adjacent and distinct sequence rearrangements were identified at a NAP1 locus in a soybean mutant. Genetic dissection and validation revealed the function of this gene in soybean trichome development. A soybean (Glycine max (L.) Merr.) gnarled trichome mutant, exhibiting stunted trichomes compared to wild-type, was identified in a fast neutron mutant population. Genetic mapping using whole genome sequencing-based bulked segregant analysis identified a 26.6 megabase interval on chromosome 20 that co-segregated with the phenotype. Comparative genomic hybridization analysis of the mutant indicated that the chromosome 20 interval included a small structural variant within the coding region of a soybean ortholog (Glyma.20G019300) of Arabidopsis Nck-Associated Protein 1 (NAP1), a regulator of actin nucleation during trichome morphogenesis. Sequence analysis of the candidate allele revealed multiple rearrangements within the coding region, including two deletions (approximately 1-2 kb each), a translocation, and an inversion. Further analyses revealed that the mutant allele perfectly co-segregated with the phenotype, and a wild-type soybean NAP1 transgene functionally complemented an Arabidopsis nap1 mutant. In addition, mapping and exon sequencing of NAP1 in a spontaneous soybean gnarled trichome mutant (T31) identified a frame shift mutation resulting in a truncation of the coding region. These data indicate that the soybean NAP1 gene is essential for proper trichome development and show the utility of the soybean fast neutron population for forward genetic approaches for identifying genes.
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Affiliation(s)
- Benjamin W Campbell
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Anna N Hofstad
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Suma Sreekanta
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Fengli Fu
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Thomas J Y Kono
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Jamie A O'Rourke
- USDA-ARS, Corn Insects and Crop Genetics Research, Iowa State University, Ames, IA, 50011, USA
| | - Carroll P Vance
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
- Department of Plant Biology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA.
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26
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Dynamics of a Novel Highly Repetitive CACTA Family in Common Bean (Phaseolus vulgaris). G3-GENES GENOMES GENETICS 2016; 6:2091-101. [PMID: 27185400 PMCID: PMC4938662 DOI: 10.1534/g3.116.028761] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Transposons are ubiquitous genomic components that play pivotal roles in plant gene and genome evolution. We analyzed two genome sequences of common bean (Phaseolus vulgaris) and identified a new CACTA transposon family named pvCACTA1. The family is extremely abundant, as more than 12,000 pvCACTA1 elements were found. To our knowledge, this is the most abundant CACTA family reported thus far. The computational and fluorescence in situ hybridization (FISH) analyses indicated that the pvCACTA1 elements were concentrated in terminal regions of chromosomes and frequently generated AT-rich 3 bp target site duplications (TSD, WWW, W is A or T). Comparative analysis of the common bean genomes from two domesticated genetic pools revealed that new insertions or excisions of pvCACTA1 elements occurred after the divergence of the two common beans, and some of the polymorphic elements likely resulted in variation in gene sequences. pvCACTA1 elements were detected in related species but not outside the Phaseolus genus. We calculated the molecular evolutionary rate of pvCACTA1 transposons using orthologous elements that indicated that most transposition events likely occurred before the divergence of the two gene pools. These results reveal unique features and evolution of this new transposon family in the common bean genome.
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27
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Campbell BW, Stupar RM. Soybean (Glycine max) Mutant and Germplasm Resources: Current Status and Future Prospects. ACTA ACUST UNITED AC 2016; 1:307-327. [PMID: 30775866 DOI: 10.1002/cppb.20015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Genetic bottlenecks during domestication and modern breeding limited the genetic diversity of soybean (Glycine max (L.) Merr.). Therefore, expanding and diversifying soybean genetic resources is a major priority for the research community. These resources, consisting of natural and induced genetic variants, are valuable tools for improving soybean and furthering soybean biological knowledge. During the twentieth century, researchers gathered a wealth of genetic variation in the forms of landraces, Glycine soja accessions, Glycine tertiary germplasm, and the U.S. Department of Agriculture (USDA) Type and Isoline Collections. During the twenty-first century, soybean researchers have added several new genetic and genomic resources. These include the reference genome sequence, genotype data for the USDA soybean germplasm collection, next-generation mapping populations, new irradiation and transposon-based mutagenesis populations, and designer nuclease platforms for genome engineering. This paper briefly surveys the publicly accessible soybean genetic resources currently available or in development and provides recommendations for developing such genetic resources in the future. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Benjamin W Campbell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota
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28
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Mustafiz A, Kumari S, Karan R. Ascribing Functions to Genes: Journey Towards Genetic Improvement of Rice Via Functional Genomics. Curr Genomics 2016; 17:155-76. [PMID: 27252584 PMCID: PMC4869004 DOI: 10.2174/1389202917666160202215135] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 07/01/2015] [Accepted: 07/06/2015] [Indexed: 11/22/2022] Open
Abstract
Rice, one of the most important cereal crops for mankind, feeds more than half the world population. Rice has been heralded as a model cereal owing to its small genome size, amenability to easy transformation, high synteny to other cereal crops and availability of complete genome sequence. Moreover, sequence wealth in rice is getting more refined and precise due to resequencing efforts. This humungous resource of sequence data has confronted research fraternity with a herculean challenge as well as an excellent opportunity to functionally validate expressed as well as regulatory portions of the genome. This will not only help us in understanding the genetic basis of plant architecture and physiology but would also steer us towards developing improved cultivars. No single technique can achieve such a mammoth task. Functional genomics through its diverse tools viz. loss and gain of function mutants, multifarious omics strategies like transcriptomics, proteomics, metabolomics and phenomics provide us with the necessary handle. A paradigm shift in technological advances in functional genomics strategies has been instrumental in generating considerable amount of information w.r.t functionality of rice genome. We now have several databases and online resources for functionally validated genes but despite that we are far from reaching the desired milestone of functionally characterizing each and every rice gene. There is an urgent need for a common platform, for information already available in rice, and collaborative efforts between researchers in a concerted manner as well as healthy public-private partnership, for genetic improvement of rice crop better able to handle the pressures of climate change and exponentially increasing population.
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Affiliation(s)
- Ananda Mustafiz
- South Asian University, Akbar Bhawan, Chanakyapuri, New Delhi
| | - Sumita Kumari
- Sher-e-Kashmir University of Agriculture Sciences and Technology, Jammu 180009, India
| | - Ratna Karan
- Agronomy Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville - 32611, Florida, USA
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29
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Anderson JE, Michno JM, Kono TJY, Stec AO, Campbell BW, Curtin SJ, Stupar RM. Genomic variation and DNA repair associated with soybean transgenesis: a comparison to cultivars and mutagenized plants. BMC Biotechnol 2016; 16:41. [PMID: 27176220 PMCID: PMC4866027 DOI: 10.1186/s12896-016-0271-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 05/04/2016] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The safety of mutagenized and genetically transformed plants remains a subject of scrutiny. Data gathered and communicated on the phenotypic and molecular variation induced by gene transfer technologies will provide a scientific-based means to rationally address such concerns. In this study, genomic structural variation (e.g. large deletions and duplications) and single nucleotide polymorphism rates were assessed among a sample of soybean cultivars, fast neutron-derived mutants, and five genetically transformed plants developed through Agrobacterium based transformation methods. RESULTS On average, the number of genes affected by structural variations in transgenic plants was one order of magnitude less than that of fast neutron mutants and two orders of magnitude less than the rates observed between cultivars. Structural variants in transgenic plants, while rare, occurred adjacent to the transgenes, and at unlinked loci on different chromosomes. DNA repair junctions at both transgenic and unlinked sites were consistent with sequence microhomology across breakpoints. The single nucleotide substitution rates were modest in both fast neutron and transformed plants, exhibiting fewer than 100 substitutions genome-wide, while inter-cultivar comparisons identified over one-million single nucleotide polymorphisms. CONCLUSIONS Overall, these patterns provide a fresh perspective on the genomic variation associated with high-energy induced mutagenesis and genetically transformed plants. The genetic transformation process infrequently results in novel genetic variation and these rare events are analogous to genetic variants occurring spontaneously, already present in the existing germplasm, or induced through other types of mutagenesis. It remains unclear how broadly these results can be applied to other crops or transformation methods.
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Affiliation(s)
- Justin E Anderson
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Jean-Michel Michno
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Thomas J Y Kono
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Adrian O Stec
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Benjamin W Campbell
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Shaun J Curtin
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Robert M Stupar
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA.
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30
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Kanizay L, Jacobs T, Hancock CN. A transgenic, visual screenable marker for soybean seeds. Transgenic Res 2016; 25:187-93. [PMID: 26660729 DOI: 10.1007/s11248-015-9922-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 11/20/2015] [Indexed: 10/22/2022]
Abstract
Most soybean cultivars produce buff colored seeds due to a seed coat specific siRNA mechanism. This phenomenon is specifically limited to the seed coat and produces a strong visual effect, thus, a strategy to evade the silencing was used to produce a maternal transgenic marker for soybeans. Expression of a rice chalcone synthase transgene with little DNA sequence homology to the soybean siRNAs resulted in dark colored seed coats. This phenotype is the result of anthocyanin pigment production and does not appear to affect other tissues. This novel approach for producing an easily scored transgenic marker for soybean will facilitate high-throughput screening and analysis of transgenic soybean.
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Affiliation(s)
- Lisa Kanizay
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Rd, Athens, GA, 30602, USA
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, 111 Riverbend Rd, Athens, GA, 30602, USA
| | - Thomas Jacobs
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Rd, Athens, GA, 30602, USA
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, 111 Riverbend Rd, Athens, GA, 30602, USA
| | - C Nathan Hancock
- Department of Biology and Geology, University of South Carolina Aiken, 471 University Parkway, Aiken, SC, 29801, USA.
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31
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Jacobs TB, Lawler NJ, LaFayette PR, Vodkin LO, Parrott WA. Simple gene silencing using the trans-acting siRNA pathway. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:117-27. [PMID: 25816689 DOI: 10.1111/pbi.12362] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 02/14/2015] [Accepted: 02/19/2015] [Indexed: 05/27/2023]
Abstract
In plants, particular micro-RNAs (miRNAs) induce the production of a class of small interfering RNAs (siRNA) called trans-acting siRNA (ta-siRNA) that lead to gene silencing. A single miRNA target is sufficient for the production of ta-siRNAs, which target can be incorporated into a vector to induce the production of siRNAs, and ultimately gene silencing. The term miRNA-induced gene silencing (MIGS) has been used to describe such vector systems in Arabidopsis. Several ta-siRNA loci have been identified in soybean, but, prior to this work, few of the inducing miRNAs have been experimentally validated, much less used to silence genes. Nine ta-siRNA loci and their respective miRNA targets were identified, and the abundance of the inducing miRNAs varies dramatically in different tissues. The miRNA targets were experimentally verified by silencing a transgenic GFP gene and two endogenous genes in hairy roots and transgenic plants. Small RNAs were produced in patterns consistent with the utilization of the ta-siRNA pathway. A side-by-side experiment demonstrated that MIGS is as effective at inducing gene silencing as traditional hairpin vectors in soybean hairy roots. Soybean plants transformed with MIGS vectors produced siRNAs and silencing was observed in the T1 generation. These results complement previous reports in Arabidopsis by demonstrating that MIGS is an efficient way to produce siRNAs and induce gene silencing in other species, as shown with soybean. The miRNA targets identified here are simple to incorporate into silencing vectors and offer an effective and efficient alternative to other gene silencing strategies.
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Affiliation(s)
- Thomas B Jacobs
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Noah J Lawler
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Peter R LaFayette
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, USA
| | - Lila O Vodkin
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Wayne A Parrott
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, USA
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32
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Curtin SJ, Michno JM, Campbell BW, Gil-Humanes J, Mathioni SM, Hammond R, Gutierrez-Gonzalez JJ, Donohue RC, Kantar MB, Eamens AL, Meyers BC, Voytas DF, Stupar RM. MicroRNA Maturation and MicroRNA Target Gene Expression Regulation Are Severely Disrupted in Soybean dicer-like1 Double Mutants. G3 (BETHESDA, MD.) 2015; 6:423-33. [PMID: 26681515 PMCID: PMC4751560 DOI: 10.1534/g3.115.022137] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 12/07/2015] [Indexed: 01/06/2023]
Abstract
Small nonprotein-coding microRNAs (miRNAs) are present in most eukaryotes and are central effectors of RNA silencing-mediated mechanisms for gene expression regulation. In plants, DICER-LIKE1 (DCL1) is the founding member of a highly conserved family of RNase III-like endonucleases that function as core machinery proteins to process hairpin-like precursor transcripts into mature miRNAs, small regulatory RNAs, 21-22 nucleotides in length. Zinc finger nucleases (ZFNs) were used to generate single and double-mutants of putative soybean DCL1 homologs, DCL1a and DCL1b, to confirm their functional role(s) in the soybean miRNA pathway. Neither DCL1 single mutant, dcl1a or dcl1b plants, exhibited a pronounced morphological or molecular phenotype. However, the dcl1a/dcl1b double mutant expressed a strong morphological phenotype, characterized by reduced seed size and aborted seedling development, in addition to defective miRNA precursor transcript processing efficiency and deregulated miRNA target gene expression. Together, these findings indicate that the two soybean DCL1 paralogs, DCL1a and DCL1b, largely play functionally redundant roles in the miRNA pathway and are essential for normal plant development.
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Affiliation(s)
- Shaun J Curtin
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, 55108
| | - Jean-Michel Michno
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, 55108
| | - Benjamin W Campbell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, 55108
| | - Javier Gil-Humanes
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55455 Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Sandra M Mathioni
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19711
| | - Reza Hammond
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19711
| | | | - Ryan C Donohue
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, 55108
| | - Michael B Kantar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, 55108
| | - Andrew L Eamens
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Blake C Meyers
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19711
| | - Daniel F Voytas
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55455 Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, 55108
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Gilbert DM, Bridges MC, Strother AE, Burckhalter CE, Burnette JM, Hancock CN. Precise repair of mPing excision sites is facilitated by target site duplication derived microhomology. Mob DNA 2015; 6:15. [PMID: 26347803 PMCID: PMC4561436 DOI: 10.1186/s13100-015-0046-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 08/28/2015] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND A key difference between the Tourist and Stowaway families of miniature inverted repeat transposable elements (MITEs) is the manner in which their excision alters the genome. Upon excision, Stowaway-like MITEs and the associated Mariner elements usually leave behind a small duplication and short sequences from the end of the element. These small insertions or deletions known as "footprints" can potentially disrupt coding or regulatory sequences. In contrast, Tourist-like MITEs and the associated PIF/Pong/Harbinger elements generally excise precisely, returning the genome to its original state. The purpose of this study was to determine the mechanisms underlying these excision differences, including the role of the host DNA repair mechanisms. RESULTS The transposition of the Tourist-like element, mPing, and the Stowaway-like element, 14T32, were evaluated using yeast transposition assays. Assays performed in yeast strains lacking non-homologous end joining (NHEJ) enzymes indicated that the excision sites of both elements were primarily repaired by NHEJ. Altering the target site duplication (TSD) sequences that flank these elements reduced the transposition frequency. Using yeast strains with the ability to repair the excision site by homologous repair showed that some TSD changes disrupt excision of the element. Changing the ends of mPing to produce non-matching TSDs drastically reduced repair of the excision site and resulted in increased generation of footprints. CONCLUSIONS Together these results indicate that the difference in Tourist and Stowaway excision sites results from transposition mechanism characteristics. The TSDs of both elements play a role in element excision, but only the mPing TSDs actively participate in excision site repair. Our data suggests that Tourist-like elements excise with staggered cleavage of the TSDs, which provides microhomology that facilitates precise repair. This slight modification in the transposition mechanism results in more efficient repair of the double stranded break, and thus, may be less harmful to host genomes by disrupting fewer genes.
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Affiliation(s)
- David M Gilbert
- Department of Biology and Geology, University of South Carolina Aiken, 471 University Parkway, Aiken, SC 29801 USA
| | - M Catherine Bridges
- Present Address: Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC 29425 USA
| | - Ashley E Strother
- Department of Biology and Geology, University of South Carolina Aiken, 471 University Parkway, Aiken, SC 29801 USA
| | - Courtney E Burckhalter
- Department of Biology and Geology, University of South Carolina Aiken, 471 University Parkway, Aiken, SC 29801 USA
| | - James M Burnette
- Present Address: College of Natural and Agricultural Sciences, University of California Riverside, Riverside, CA 92521 USA
| | - C Nathan Hancock
- Department of Biology and Geology, University of South Carolina Aiken, 471 University Parkway, Aiken, SC 29801 USA
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Liu JZ, Graham MA, Pedley KF, Whitham SA. Gaining insight into soybean defense responses using functional genomics approaches. Brief Funct Genomics 2015; 14:283-90. [PMID: 25832523 DOI: 10.1093/bfgp/elv009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
Soybean pathogens significantly impact yield, resulting in over $4 billion dollars in lost revenue annually in the United States. Despite the deployment of improved soybean cultivars, pathogens continue to evolve to evade plant defense responses. Thus, there is an urgent need to identify and characterize gene networks controlling defense responses to harmful pathogens. In this review, we focus on major advances that have been made in identifying the genes and gene networks regulating defense responses with an emphasis on soybean-pathogen interactions that have been amenable to gene function analyses using gene silencing technologies. Further we describe new research striving to identify genes involved in durable broad-spectrum resistance. Finally, we consider future prospects for functional genomic studies in soybean and demonstrate that understanding soybean disease and stress tolerance will be expedited at an unprecedented pace.
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Gong L, Masonbrink RE, Grover CE, Renny-Byfield S, Wendel JF. A Cluster of Recently Inserted Transposable Elements Associated with siRNAs in Gossypium raimondii. THE PLANT GENOME 2015; 8:eplantgenome2014.11.0088. [PMID: 33228305 DOI: 10.3835/plantgenome2014.11.0088] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 02/06/2015] [Indexed: 06/11/2023]
Abstract
Stabilization of transposable element (TE) copy number involves the biosynthesis of short silencing RNAs (siRNAs) and further initialization of siRNA-mediated TE silencing. To gain insight into the relationship between the biosynthesis of siRNAs and their source TEs, we examined the co-evolutionary dynamics and expression of these two entities by characterizing the siRNA distribution across the genome of Gossypium raimondii Ulbr. We identified an unusual region at the 3' end of chromosome 1 with significantly enriched siRNA coverage. Analysis of the correlation pattern between uniquely mapped siRNAs and those mapping to multiple regions implicated active biogenesis of siRNAs from these potential young TEs. Furthermore, divergence estimates of TEs within this region confirmed that the majority of TEs are young. Active transcription of the source TEs and their positive correlation with expressed siRNAs indicates that sufficient expression of TEs may be necessary to generate siRNAs and maintain the silenced state of recently transposed TEs.
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Affiliation(s)
- Lei Gong
- Dep. of Ecology, Evolution and Organismal Biology, Iowa State Univ., Ames, IA, 50011, USA
| | - Rick E Masonbrink
- Dep. of Ecology, Evolution and Organismal Biology, Iowa State Univ., Ames, IA, 50011, USA
| | - Corrinne E Grover
- Dep. of Ecology, Evolution and Organismal Biology, Iowa State Univ., Ames, IA, 50011, USA
| | - Simon Renny-Byfield
- Dep. of Ecology, Evolution and Organismal Biology, Iowa State Univ., Ames, IA, 50011, USA
| | - Jonathan F Wendel
- Dep. of Ecology, Evolution and Organismal Biology, Iowa State Univ., Ames, IA, 50011, USA
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36
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Jacobs TB, LaFayette PR, Schmitz RJ, Parrott WA. Targeted genome modifications in soybean with CRISPR/Cas9. BMC Biotechnol 2015. [PMID: 25879861 DOI: 10.1186/s12896-12015-10131-12892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2023] Open
Abstract
BACKGROUND The ability to selectively alter genomic DNA sequences in vivo is a powerful tool for basic and applied research. The CRISPR/Cas9 system precisely mutates DNA sequences in a number of organisms. Here, the CRISPR/Cas9 system is shown to be effective in soybean by knocking-out a green fluorescent protein (GFP) transgene and modifying nine endogenous loci. RESULTS Targeted DNA mutations were detected in 95% of 88 hairy-root transgenic events analyzed. Bi-allelic mutations were detected in events transformed with eight of the nine targeting vectors. Small deletions were the most common type of mutation produced, although SNPs and short insertions were also observed. Homoeologous genes were successfully targeted singly and together, demonstrating that CRISPR/Cas9 can both selectively, and generally, target members of gene families. Somatic embryo cultures were also modified to enable the production of plants with heritable mutations, with the frequency of DNA modifications increasing with culture time. A novel cloning strategy and vector system based on In-Fusion® cloning was developed to simplify the production of CRISPR/Cas9 targeting vectors, which should be applicable for targeting any gene in any organism. CONCLUSIONS The CRISPR/Cas9 is a simple, efficient, and highly specific genome editing tool in soybean. Although some vectors are more efficient than others, it is possible to edit duplicated genes relatively easily. The vectors and methods developed here will be useful for the application of CRISPR/Cas9 to soybean and other plant species.
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Affiliation(s)
- Thomas B Jacobs
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, Georgia, 30602, USA.
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA.
- Present address: Boyce Thompson Institute for Plant Research, Ithaca, NY, 14853, USA.
| | - Peter R LaFayette
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA.
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA.
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA.
| | - Wayne A Parrott
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, Georgia, 30602, USA.
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA.
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA.
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Jacobs TB, LaFayette PR, Schmitz RJ, Parrott WA. Targeted genome modifications in soybean with CRISPR/Cas9. BMC Biotechnol 2015; 15:16. [PMID: 25879861 PMCID: PMC4365529 DOI: 10.1186/s12896-015-0131-2] [Citation(s) in RCA: 306] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 02/27/2015] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND The ability to selectively alter genomic DNA sequences in vivo is a powerful tool for basic and applied research. The CRISPR/Cas9 system precisely mutates DNA sequences in a number of organisms. Here, the CRISPR/Cas9 system is shown to be effective in soybean by knocking-out a green fluorescent protein (GFP) transgene and modifying nine endogenous loci. RESULTS Targeted DNA mutations were detected in 95% of 88 hairy-root transgenic events analyzed. Bi-allelic mutations were detected in events transformed with eight of the nine targeting vectors. Small deletions were the most common type of mutation produced, although SNPs and short insertions were also observed. Homoeologous genes were successfully targeted singly and together, demonstrating that CRISPR/Cas9 can both selectively, and generally, target members of gene families. Somatic embryo cultures were also modified to enable the production of plants with heritable mutations, with the frequency of DNA modifications increasing with culture time. A novel cloning strategy and vector system based on In-Fusion® cloning was developed to simplify the production of CRISPR/Cas9 targeting vectors, which should be applicable for targeting any gene in any organism. CONCLUSIONS The CRISPR/Cas9 is a simple, efficient, and highly specific genome editing tool in soybean. Although some vectors are more efficient than others, it is possible to edit duplicated genes relatively easily. The vectors and methods developed here will be useful for the application of CRISPR/Cas9 to soybean and other plant species.
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Affiliation(s)
- Thomas B Jacobs
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, Georgia, 30602, USA.
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA.
- Present address: Boyce Thompson Institute for Plant Research, Ithaca, NY, 14853, USA.
| | - Peter R LaFayette
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA.
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA.
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA.
| | - Wayne A Parrott
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, Georgia, 30602, USA.
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA.
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA.
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Kanizay LB, Jacobs TB, Gillespie K, Newsome JA, Spaid BN, Parrott WA. HtStuf: High-Throughput Sequencing to Locate Unknown DNA Junction Fragments. THE PLANT GENOME 2015; 8:eplantgenome2014.10.0070. [PMID: 33228280 DOI: 10.3835/plantgenome2014.10.0070] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 12/15/2014] [Indexed: 06/11/2023]
Abstract
Advances in high-throughput sequencing have led to many new technologies for assessing genomes and population diversity. In spite of this, inexpensive and technically simple methods for efficiently pinpointing the location of transgenes and other specific sequences in large genomes are lacking. Here we report the development of a modified TA cloning and Illumina sequencing method called high-throughput sequencing to locate unmapped DNA fragments (HtStuf). Transgenic insertion sites were identified and confirmed in nine out of 10 transgenic soybean [Glycine max (L.) Merr.] lines, and major rearrangements of the transgene were detected in these lines. Additionally this method was used to map insertions of the introduced DNA transposon, mPing, in four T6 lines derived from a single event. Fifteen of the mPing insertion sites were validated with polymerase chain reaction. Together, these data demonstrate the simplicity and effectiveness of this novel sequencing method.
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Affiliation(s)
- Lisa B Kanizay
- Center for Applied Genetic Technologies, Univ. of Georgia, Athens, GA, 30602
| | - Thomas B Jacobs
- Institute for Plant Breeding, Genetics and Genomics, Univ. of Georgia, Athens, GA, 30602
- Center for Applied Genetic Technologies, Univ. of Georgia, Athens, GA, 30602
| | - Kevin Gillespie
- Center for Applied Genetic Technologies, Univ. of Georgia, Athens, GA, 30602
| | - Jade A Newsome
- Center for Applied Genetic Technologies, Univ. of Georgia, Athens, GA, 30602
| | - Brittany N Spaid
- Center for Applied Genetic Technologies, Univ. of Georgia, Athens, GA, 30602
| | - Wayne A Parrott
- Institute for Plant Breeding, Genetics and Genomics, Univ. of Georgia, Athens, GA, 30602
- Dep. of Crop and Soil Sciences, Univ. of Georgia, Athens, GA, 30602
- Center for Applied Genetic Technologies, Univ. of Georgia, Athens, GA, 30602
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Naito K, Monden Y, Yasuda K, Saito H, Okumoto Y. mPing: The bursting transposon. BREEDING SCIENCE 2014; 64:109-14. [PMID: 25053919 PMCID: PMC4065317 DOI: 10.1270/jsbbs.64.109] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 01/30/2014] [Indexed: 05/25/2023]
Abstract
Though transposable elements (TEs) have been considered as an efficient source of evolution, it has never been possible to test this hypothesis because most of TE insertions had occurred millions of years ago, or because currently active TEs have very few copies in a host genome. However, mPing, the first active DNA transposon in rice, was revealed to hold a key to answer this question. mPing has attained high copy numbers and still retained very high activity in a traditional rice strain, which enabled direct observation of behavior and impact of a bursting TE. A comprehensive analysis of mPing insertion sites has revealed it avoids exons but prefers promoter regions and thus moderately affects transcription of neighboring genes. Some of the mPing insertions have introduced possibly useful expression profile to adjacent genes that indicated TE's potential in de novo formation of gene regulatory network.
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Affiliation(s)
- Ken Naito
- Genetic Resource Center, National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Yuki Monden
- Graduate School of Environmental and life Science, Okayama University,
3-1-1 Tsushima-naka, Kita, Okayama 700-8530,
Japan
| | - Kanako Yasuda
- Department of Agriculture, Kyoto University,
Kitashirakawa Oiwake, Sakyo, Kyoto 606-8502,
Japan
| | - Hiroki Saito
- Department of Agriculture, Kyoto University,
Kitashirakawa Oiwake, Sakyo, Kyoto 606-8502,
Japan
| | - Yutaka Okumoto
- Department of Agriculture, Kyoto University,
Kitashirakawa Oiwake, Sakyo, Kyoto 606-8502,
Japan
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40
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Genome-wide comparative analysis of 20 miniature inverted-repeat transposable element families in Brassica rapa and B. oleracea. PLoS One 2014; 9:e94499. [PMID: 24747717 PMCID: PMC3991616 DOI: 10.1371/journal.pone.0094499] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 03/17/2014] [Indexed: 12/25/2022] Open
Abstract
Miniature inverted-repeat transposable elements (MITEs) are ubiquitous, non-autonomous class II transposable elements. Here, we conducted genome-wide comparative analysis of 20 MITE families in B. rapa, B. oleracea, and Arabidopsis thaliana. A total of 5894 and 6026 MITE members belonging to the 20 families were found in the whole genome pseudo-chromosome sequences of B. rapa and B. oleracea, respectively. Meanwhile, only four of the 20 families, comprising 573 members, were identified in the Arabidopsis genome, indicating that most of the families were activated in the Brassica genus after divergence from Arabidopsis. Copy numbers varied from 4 to 1459 for each MITE family, and there was up to 6-fold variation between B. rapa and B. oleracea. In particular, analysis of intact members showed that whereas eleven families were present in similar copy numbers in B. rapa and B. oleracea, nine families showed copy number variation ranging from 2- to 16-fold. Four of those families (BraSto-3, BraTo-3, 4, 5) were more abundant in B. rapa, and the other five (BraSto-1, BraSto-4, BraTo-1, 7 and BraHAT-1) were more abundant in B. oleracea. Overall, 54% and 51% of the MITEs resided in or within 2 kb of a gene in the B. rapa and B. oleracea genomes, respectively. Notably, 92 MITEs were found within the CDS of annotated genes, suggesting that MITEs might play roles in diversification of genes in the recently triplicated Brassica genome. MITE insertion polymorphism (MIP) analysis of 289 MITE members showed that 52% and 23% were polymorphic at the inter- and intra-species levels, respectively, indicating that there has been recent MITE activity in the Brassica genome. These recently activated MITE families with abundant MIP will provide useful resources for molecular breeding and identification of novel functional genes arising from MITE insertion.
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Appels R, Nystrom-Persson J, Keeble-Gagnere G. Advances in genome studies in plants and animals. Funct Integr Genomics 2014; 14:1-9. [PMID: 24626952 PMCID: PMC3968518 DOI: 10.1007/s10142-014-0364-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 02/19/2014] [Indexed: 01/30/2023]
Abstract
The area of plant and animal genomics covers the entire suite of issues in biology because it aims to determine the structure and function of genetic material. Although specific issues define research advances at an organism level, it is evident that many of the fundamental features of genome structure and the translation of encoded information to function share common ground. The Plant and Animal Genome (PAG) conference held in San Diego (California), in January each year provides an overview across all organisms at the genome level, and often it is evident that investments in the human area provide leadership, applications, and discoveries for researchers studying other organisms. This mini-review utilizes the plenary lectures as a basis for summarizing the trends in the genome-level studies of organisms, and the lectures include presentations by Ewan Birney (EBI, UK), Eric Green (NIH, USA), John Butler (NIST, USA), Elaine Mardis (Washington, USA), Caroline Dean (John Innes Centre, UK), Trudy Mackay (NC State University, USA), Sue Wessler (UC Riverside, USA), and Patrick Wincker (Genoscope, France). The work reviewed is based on published papers. Where unpublished information is cited, permission to include the information in this manuscript was obtained from the presenters.
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Affiliation(s)
- R Appels
- Veterinary and Life Sciences, Murdoch University, 90 South Street, Murdoch, Perth, WA, 6150, Australia,
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42
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Park KC, Son JH, Lee SII, Kim KS, Chang YS, Kim NS. Pong-like elements in Arabidopsis and Brassica rapa: its regulation of F-box protein gene in different ecotypes of Arabidopsis thaliana. Genes Genomics 2013. [DOI: 10.1007/s13258-013-0129-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Fattash I, Bhardwaj P, Hui C, Yang G. A rice Stowaway MITE for gene transfer in yeast. PLoS One 2013; 8:e64135. [PMID: 23704977 PMCID: PMC3660474 DOI: 10.1371/journal.pone.0064135] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Accepted: 04/11/2013] [Indexed: 02/06/2023] Open
Abstract
Miniature inverted repeat transposable elements (MITEs) lack protein coding capacity and often share very limited sequence similarity with potential autonomous elements. Their capability of efficient transposition and dramatic amplification led to the proposition that MITEs are an untapped rich source of materials for transposable element (TE) based genetic tools. To test the concept of using MITE sequence in gene transfer, a rice Stowaway MITE previously shown to excise efficiently in yeast was engineered to carry cargo genes (neo and gfp) for delivery into the budding yeast genome. Efficient excision of the cargo gene cassettes was observed even though the excision frequency generally decreases with the increase of the cargo sizes. Excised elements insert into new genomic loci efficiently, with about 65% of the obtained insertion sites located in genes. Elements at the primary insertion sites can be remobilized, frequently resulting in copy number increase of the element. Surprisingly, the orientation of a cargo gene (neo) on a construct bearing dual reporter genes (gfp and neo) was found to have a dramatic effect on transposition frequency. These results demonstrated the concept that MITE sequences can be useful in engineering genetic tools to deliver cargo genes into eukaryotic genomes.
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Affiliation(s)
- Isam Fattash
- Department of Biology, University of Toronto Mississauga, Mississauga, Canada
| | - Priyanka Bhardwaj
- Department of Biology, University of Toronto Mississauga, Mississauga, Canada
| | - Caleb Hui
- Department of Biology, University of Toronto Mississauga, Mississauga, Canada
| | - Guojun Yang
- Department of Biology, University of Toronto Mississauga, Mississauga, Canada
- * E-mail:
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Wang N, Long T, Yao W, Xiong L, Zhang Q, Wu C. Mutant resources for the functional analysis of the rice genome. MOLECULAR PLANT 2013; 6:596-604. [PMID: 23204502 DOI: 10.1093/mp/sss142] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Rice is one of the most important crops worldwide, both as a staple food and as a model system for genomic research. In order to systematically assign functions to all predicted genes in the rice genome, a large number of rice mutant lines, including those created by T-DNA insertion, Ds/dSpm tagging, Tos17 tagging, and chemical/irradiation mutagenesis, have been generated by groups around the world. In this study, we have reviewed the current status of mutant resources for functional analysis of the rice genome. A total of 246 566 flanking sequence tags from rice mutant libraries with T-DNA, Ds/dSpm, or Tos17 insertion have been collected and analyzed. The results show that, among 211 470 unique hits, inserts located in the genic region account for 68.16%, and 60.49% of nuclear genes contain at least one insertion. Currently, 57% of non-transposable-element-related genes in rice have insertional tags. In addition, chemical/irradiation-induced rice mutant libraries have contributed a lot to both gene identification and new technology for the identification of mutant sites. In this review, we summarize how these tools have been used to generate a large collection of mutants. In addition, we discuss the merits of classic mutation strategies. In order to achieve saturation of mutagenesis in rice, DNA targeting, and new resources like RiceFox for gene functional identification are reviewed from a perspective of the future generation of rice mutant resources.
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Affiliation(s)
- Nili Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
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Cui Y, Barampuram S, Stacey MG, Hancock CN, Findley S, Mathieu M, Zhang Z, Parrott WA, Stacey G. Tnt1 retrotransposon mutagenesis: a tool for soybean functional genomics. PLANT PHYSIOLOGY 2013; 161:36-47. [PMID: 23124322 PMCID: PMC3532266 DOI: 10.1104/pp.112.205369] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 10/30/2012] [Indexed: 05/23/2023]
Abstract
Insertional mutagenesis is a powerful tool for determining gene function in both model and crop plant species. Tnt1, the transposable element of tobacco (Nicotiana tabacum) cell type 1, is a retrotransposon that replicates via an RNA copy that is reverse transcribed and integrated elsewhere in the plant genome. Based on studies in a variety of plants, Tnt1 appears to be inactive in normal plant tissue but can be reactivated by tissue culture. Our goal was to evaluate the utility of the Tnt1 retrotransposon as a mutagenesis strategy in soybean (Glycine max). Experiments showed that the Tnt1 element was stably transformed into soybean plants by Agrobacterium tumefaciens-mediated transformation. Twenty-seven independent transgenic lines carrying Tnt1 insertions were generated. Southern-blot analysis revealed that the copy number of transposed Tnt1 elements ranged from four to 19 insertions, with an average of approximately eight copies per line. These insertions showed Mendelian segregation and did not transpose under normal growth conditions. Analysis of 99 Tnt1 flanking sequences revealed insertions into 62 (62%) annotated genes, indicating that the element preferentially inserts into protein-coding regions. Tnt1 insertions were found in all 20 soybean chromosomes, indicating that Tnt1 transposed throughout the soybean genome. Furthermore, fluorescence in situ hybridization experiments validated that Tnt1 inserted into multiple chromosomes. Passage of transgenic lines through two different tissue culture treatments resulted in Tnt1 transposition, significantly increasing the number of insertions per line. Thus, our data demonstrate the Tnt1 retrotransposon to be a powerful system that can be used for effective large-scale insertional mutagenesis in soybean.
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Affiliation(s)
- Yaya Cui
- Divisions of Plant Sciences and Biochemistry, National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri 65211 (Y.C., S.B., M.G.S., S.F., M.M., Z.Z., G.S.); Department of Biology and Geology, University of South Carolina, Aiken, South Carolina 29801 (C.N.H.); and Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602–7272 (W.A.P.)
| | - Shyam Barampuram
- Divisions of Plant Sciences and Biochemistry, National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri 65211 (Y.C., S.B., M.G.S., S.F., M.M., Z.Z., G.S.); Department of Biology and Geology, University of South Carolina, Aiken, South Carolina 29801 (C.N.H.); and Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602–7272 (W.A.P.)
| | - Minviluz G. Stacey
- Divisions of Plant Sciences and Biochemistry, National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri 65211 (Y.C., S.B., M.G.S., S.F., M.M., Z.Z., G.S.); Department of Biology and Geology, University of South Carolina, Aiken, South Carolina 29801 (C.N.H.); and Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602–7272 (W.A.P.)
| | - C. Nathan Hancock
- Divisions of Plant Sciences and Biochemistry, National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri 65211 (Y.C., S.B., M.G.S., S.F., M.M., Z.Z., G.S.); Department of Biology and Geology, University of South Carolina, Aiken, South Carolina 29801 (C.N.H.); and Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602–7272 (W.A.P.)
| | - Seth Findley
- Divisions of Plant Sciences and Biochemistry, National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri 65211 (Y.C., S.B., M.G.S., S.F., M.M., Z.Z., G.S.); Department of Biology and Geology, University of South Carolina, Aiken, South Carolina 29801 (C.N.H.); and Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602–7272 (W.A.P.)
| | - Melanie Mathieu
- Divisions of Plant Sciences and Biochemistry, National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri 65211 (Y.C., S.B., M.G.S., S.F., M.M., Z.Z., G.S.); Department of Biology and Geology, University of South Carolina, Aiken, South Carolina 29801 (C.N.H.); and Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602–7272 (W.A.P.)
| | - Zhanyuan Zhang
- Divisions of Plant Sciences and Biochemistry, National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri 65211 (Y.C., S.B., M.G.S., S.F., M.M., Z.Z., G.S.); Department of Biology and Geology, University of South Carolina, Aiken, South Carolina 29801 (C.N.H.); and Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602–7272 (W.A.P.)
| | - Wayne A. Parrott
- Divisions of Plant Sciences and Biochemistry, National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri 65211 (Y.C., S.B., M.G.S., S.F., M.M., Z.Z., G.S.); Department of Biology and Geology, University of South Carolina, Aiken, South Carolina 29801 (C.N.H.); and Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602–7272 (W.A.P.)
| | - Gary Stacey
- Divisions of Plant Sciences and Biochemistry, National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri 65211 (Y.C., S.B., M.G.S., S.F., M.M., Z.Z., G.S.); Department of Biology and Geology, University of South Carolina, Aiken, South Carolina 29801 (C.N.H.); and Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602–7272 (W.A.P.)
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Curtin SJ, Kantar MB, Yoon HW, Whaley AM, Schlueter JA, Stupar RM. Co-expression of soybean Dicer-like genes in response to stress and development. Funct Integr Genomics 2012; 12:671-82. [PMID: 22527487 DOI: 10.1007/s10142-012-0278-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 03/15/2012] [Accepted: 03/21/2012] [Indexed: 01/03/2023]
Abstract
Regulation of gene transcription and post-transcriptional processes is critical for proper development, genome integrity, and stress responses in plants. Many genes involved in the key processes of transcriptional and post-transcriptional regulation have been well studied in model diploid organisms. However, gene and genome duplication may alter the function of the genes involved in these processes. To address this question, we assayed the stress-induced transcription patterns of duplicated gene pairs involved in RNAi and DNA methylation processes in the paleopolyploid soybean. Real-time quantitative PCR and Sequenom MassARRAY expression assays were used to profile the relative expression ratios of eight gene pairs across eight different biotic and abiotic stress conditions. The transcriptional responses to stress for genes involved in DNA methylation, RNAi processing, and miRNA processing were compared. The strongest evidence for pairwise co-expression in response to stresses was exhibited by non-paralogous Dicer-like (DCL) genes GmDCL2a-GmDCL3a and GmDCL1b-GmDCL2b, most profoundly in root tissues. Among homoeologous or paralogous DCL genes, the Dicer-like 2 (DCL2) gene pair exhibited the strongest response to stress and most conserved co-expression pattern. This was surprising because the DCL2 duplication event is more ancient than the other DCL duplications. Possible mechanisms that may be driving the DCL2 co-expression are discussed.
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Affiliation(s)
- Shaun J Curtin
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
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47
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Pislariu CI, D. Murray J, Wen J, Cosson V, Muni RRD, Wang M, A. Benedito V, Andriankaja A, Cheng X, Jerez IT, Mondy S, Zhang S, Taylor ME, Tadege M, Ratet P, Mysore KS, Chen R, Udvardi MK. A Medicago truncatula tobacco retrotransposon insertion mutant collection with defects in nodule development and symbiotic nitrogen fixation. PLANT PHYSIOLOGY 2012; 159:1686-99. [PMID: 22679222 PMCID: PMC3425206 DOI: 10.1104/pp.112.197061] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 06/01/2012] [Indexed: 05/20/2023]
Abstract
A Tnt1-insertion mutant population of Medicago truncatula ecotype R108 was screened for defects in nodulation and symbiotic nitrogen fixation. Primary screening of 9,300 mutant lines yielded 317 lines with putative defects in nodule development and/or nitrogen fixation. Of these, 230 lines were rescreened, and 156 lines were confirmed with defective symbiotic nitrogen fixation. Mutants were sorted into six distinct phenotypic categories: 72 nonnodulating mutants (Nod-), 51 mutants with totally ineffective nodules (Nod+ Fix-), 17 mutants with partially ineffective nodules (Nod+ Fix+/-), 27 mutants defective in nodule emergence, elongation, and nitrogen fixation (Nod+/- Fix-), one mutant with delayed and reduced nodulation but effective in nitrogen fixation (dNod+/- Fix+), and 11 supernodulating mutants (Nod++Fix+/-). A total of 2,801 flanking sequence tags were generated from the 156 symbiotic mutant lines. Analysis of flanking sequence tags revealed 14 insertion alleles of the following known symbiotic genes: NODULE INCEPTION (NIN), DOESN'T MAKE INFECTIONS3 (DMI3/CCaMK), ERF REQUIRED FOR NODULATION, and SUPERNUMERARY NODULES (SUNN). In parallel, a polymerase chain reaction-based strategy was used to identify Tnt1 insertions in known symbiotic genes, which revealed 25 additional insertion alleles in the following genes: DMI1, DMI2, DMI3, NIN, NODULATION SIGNALING PATHWAY1 (NSP1), NSP2, SUNN, and SICKLE. Thirty-nine Nod- lines were also screened for arbuscular mycorrhizal symbiosis phenotypes, and 30 mutants exhibited defects in arbuscular mycorrhizal symbiosis. Morphological and developmental features of several new symbiotic mutants are reported. The collection of mutants described here is a source of novel alleles of known symbiotic genes and a resource for cloning novel symbiotic genes via Tnt1 tagging.
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Affiliation(s)
| | | | - JiangQi Wen
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Viviane Cosson
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - RajaSekhara Reddy Duvvuru Muni
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Mingyi Wang
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Vagner A. Benedito
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Andry Andriankaja
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Xiaofei Cheng
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Ivone Torres Jerez
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Samuel Mondy
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Shulan Zhang
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Mark E. Taylor
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Million Tadege
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Pascal Ratet
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Kirankumar S. Mysore
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Rujin Chen
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
| | - Michael K. Udvardi
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (C.I.P., J.D.M., J.W., R.R.D.M., M.W., V.A.B., A.A., X.C., I.T.J., S.Z., M.E.T., M.T., K.S.M., R.C., M.K.U.); Department of Disease and Stress Biology, John Innes Center, Norwich NR4 7UH, United Kingdom (J.D.M.); Institut des Sciences du Végétale, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France (V.C., S.M., P.R.); Monsanto Holdings Pvt., Ltd, Monsanto Research Center, NH7, Hebbal, Bangalore 560 092, India (R.R.D.M.); Division of Plant and Soil Sciences, Davies College of Agriculture, Natural Resources, and Design, West Virginia University, Morgantown, West Virginia 26506 (V.A.B.); Badische Anilin- und Soda-Fabrik Plant Science Company, 67117 Limburgerhof, Germany (A.A.); and Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401 (M.T.)
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48
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Fukai E, Soyano T, Umehara Y, Nakayama S, Hirakawa H, Tabata S, Sato S, Hayashi M. Establishment of a Lotus japonicus gene tagging population using the exon-targeting endogenous retrotransposon LORE1. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 69:720-30. [PMID: 22014259 DOI: 10.1111/j.1365-313x.2011.04826.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
We established a gene tagging population of the model legume Lotus japonicus using an endogenous long terminal repeat (LTR) retrotransposon Lotus Retrotransposon 1 (LORE1). The population was composed of 2450 plant lines, from which a total of 4532 flanking sequence tags of LORE1 were recovered by pyrosequencing. The two-dimensional arrangement of the plant population, together with the use of multiple identifier sequences in the primers used to amplify the flanking regions, made it possible to trace insertions back to the original plant lines. The large-scale detection of new LORE1 insertion sites revealed a preference for genic regions, especially in exons of protein-coding genes, which is an interesting feature to consider in the interaction between host genomes and chromoviruses, to which LORE1 belongs, a class of retrotransposon widely distributed among plants. Forward screening of the symbiotic mutants from the population succeeded to identify five symbiotic mutants of known genes. These data suggest that LORE1 is robust as a genetic tool.
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Affiliation(s)
- Eigo Fukai
- Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
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