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Barta CE, Bolander B, Bilby SR, Brown JH, Brown RN, Duryee AM, Edelman DR, Gray CE, Gossett C, Haddock AG, Helsel MM, Jones AD, Klingseis ME, Leslie K, Miles EW, Prawitz RA. In Situ Dark Adaptation Enhances the Efficiency of DNA Extraction from Mature Pin Oak (Quercus palustris) Leaves, Facilitating the Identification of Partial Sequences of the 18S rRNA and Isoprene Synthase (IspS) Genes. PLANTS (BASEL, SWITZERLAND) 2017; 6:E52. [PMID: 29073736 PMCID: PMC5750628 DOI: 10.3390/plants6040052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 09/29/2017] [Accepted: 10/19/2017] [Indexed: 12/26/2022]
Abstract
Mature oak (Quercus spp.) leaves, although abundantly available during the plants' developmental cycle, are rarely exploited as viable sources of genomic DNA. These leaves are rich in metabolites difficult to remove during standard DNA purification, interfering with downstream molecular genetics applications. The current work assessed whether in situ dark adaptation, to deplete sugar reserves and inhibit secondary metabolite synthesis could compensate for the difficulties encountered when isolating DNA from mature leaves rich in secondary metabolites. We optimized a rapid, commercial kit based method to extract genomic DNA from dark- and light-adapted leaves. We demonstrated that in situ dark adaptation increases the yield and quality of genomic DNA obtained from mature oak leaves, yielding templates of sufficiently high quality for direct downstream applications, such as PCR amplification and gene identification. The quality of templates isolated from dark-adapted pin oak leaves particularly improved the amplification of larger fragments in our experiments. From DNA extracts prepared with our optimized method, we identified for the first time partial segments of the genes encoding 18S rRNA and isoprene synthase (IspS) from pin oak (Quercus palustris), whose full genome has not yet been sequenced.
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Affiliation(s)
- Csengele E Barta
- Department of Biology, Missouri Western State University, 4525 Downs Drive, Agenstein-Remington Halls, St. Joseph, MO 64507, USA.
| | - Bethany Bolander
- Department of Biology, Missouri Western State University, 4525 Downs Drive, Agenstein-Remington Halls, St. Joseph, MO 64507, USA.
| | - Steven R Bilby
- Department of Biology, Missouri Western State University, 4525 Downs Drive, Agenstein-Remington Halls, St. Joseph, MO 64507, USA.
| | - Jeremy H Brown
- Department of Biology, Missouri Western State University, 4525 Downs Drive, Agenstein-Remington Halls, St. Joseph, MO 64507, USA.
| | - Reid N Brown
- Department of Biology, Missouri Western State University, 4525 Downs Drive, Agenstein-Remington Halls, St. Joseph, MO 64507, USA.
| | - Alexander M Duryee
- Department of Biology, Missouri Western State University, 4525 Downs Drive, Agenstein-Remington Halls, St. Joseph, MO 64507, USA.
| | - Danielle R Edelman
- Department of Biology, Missouri Western State University, 4525 Downs Drive, Agenstein-Remington Halls, St. Joseph, MO 64507, USA.
| | - Christina E Gray
- Department of Biology, Missouri Western State University, 4525 Downs Drive, Agenstein-Remington Halls, St. Joseph, MO 64507, USA.
| | - Chandler Gossett
- Department of Biology, Missouri Western State University, 4525 Downs Drive, Agenstein-Remington Halls, St. Joseph, MO 64507, USA.
| | - Amie G Haddock
- Department of Biology, Missouri Western State University, 4525 Downs Drive, Agenstein-Remington Halls, St. Joseph, MO 64507, USA.
| | - Mackenzie M Helsel
- Department of Biology, Missouri Western State University, 4525 Downs Drive, Agenstein-Remington Halls, St. Joseph, MO 64507, USA.
| | - Alyssa D Jones
- Department of Biology, Missouri Western State University, 4525 Downs Drive, Agenstein-Remington Halls, St. Joseph, MO 64507, USA.
| | - Marissa E Klingseis
- Department of Biology, Missouri Western State University, 4525 Downs Drive, Agenstein-Remington Halls, St. Joseph, MO 64507, USA.
| | - Kalif Leslie
- Department of Biology, Missouri Western State University, 4525 Downs Drive, Agenstein-Remington Halls, St. Joseph, MO 64507, USA.
| | - Edward W Miles
- Department of Biology, Missouri Western State University, 4525 Downs Drive, Agenstein-Remington Halls, St. Joseph, MO 64507, USA.
| | - Rachael A Prawitz
- Department of Biology, Missouri Western State University, 4525 Downs Drive, Agenstein-Remington Halls, St. Joseph, MO 64507, USA.
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Russell JR, Bayer M, Booth C, Cardle L, Hackett CA, Hedley PE, Jorgensen L, Morris JA, Brennan RM. Identification, utilisation and mapping of novel transcriptome-based markers from blackcurrant (Ribes nigrum). BMC PLANT BIOLOGY 2011; 11:147. [PMID: 22035129 PMCID: PMC3217869 DOI: 10.1186/1471-2229-11-147] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 10/28/2011] [Indexed: 05/27/2023]
Abstract
BACKGROUND Deep-level second generation sequencing (2GS) technologies are now being applied to non-model species as a viable and favourable alternative to Sanger sequencing. Large-scale SNP discovery was undertaken in blackcurrant (Ribes nigrum L.) using transcriptome-based 2GS 454 sequencing on the parental genotypes of a reference mapping population, to generate large numbers of novel markers for the construction of a high-density linkage map. RESULTS Over 700,000 reads were produced, from which a total of 7,000 SNPs were found. A subset of polymorphic SNPs was selected to develop a 384-SNP OPA assay using the Illumina BeadXpress platform. Additionally, the data enabled identification of 3,000 novel EST-SSRs. The selected SNPs and SSRs were validated across diverse Ribes germplasm, including mapping populations and other selected Ribes species.SNP-based maps were developed from two blackcurrant mapping populations, incorporating 48% and 27% of assayed SNPs respectively. A relatively high proportion of visually monomorphic SNPs were investigated further by quantitative trait mapping of theta score outputs from BeadStudio analysis, and this enabled additional SNPs to be placed on the two maps. CONCLUSIONS The use of 2GS technology for the development of markers is superior to previously described methods, in both numbers of markers and biological informativeness of those markers. Whilst the numbers of reads and assembled contigs were comparable to similar sized studies of other non-model species, here a high proportion of novel genes were discovered across a wide range of putative function and localisation. The potential utility of markers developed using the 2GS approach in downstream breeding applications is discussed.
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Affiliation(s)
- Joanne R Russell
- Cell & Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Micha Bayer
- Cell & Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Clare Booth
- Cell & Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Linda Cardle
- Cell & Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Christine A Hackett
- Biomathematics and Statistics Scotland, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Pete E Hedley
- Cell & Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Linzi Jorgensen
- Cell & Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Jenny A Morris
- Cell & Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Rex M Brennan
- Cell & Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
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Hein I, Williamson S, Russell J, Powell W. Isolation of high molecular weight DNA suitable for BAC library construction from woody perennial soft-fruit species. Biotechniques 2005; 38:69-71. [PMID: 15679088 DOI: 10.2144/05381st02] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We have developed a novel nuclei extraction method that allows for the extraction of high molecular weight DNA from leaves of woody perennial soft-fruit species that contain high levels of carbohydrates and polyphenolics. The method utilizes a modified buffer system including 4% (w/v) polyvinylpyrrolidone (PVP)-10 and a combination of nylon filters and Percoll™ gradients to purify nuclei extracts prior to embedding in agarose plugs. The effectiveness of the method was demonstrated on leaves of red raspberry (Rubus idaeus) and blackcurrant (Ribes nigrum), two soft-fruit species that have shown to be recalcitrant to standard genomic DNA extraction methods. Extracted DNA was readily digested by restriction enzymes and, as shown for raspberry, suitable for bacterial artificial chromosome (BAC) library construction.
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Affiliation(s)
- Ingo Hein
- Scottish Crop Research Institute, Programme of Genome Dynamics, Invergowrie, Dundee, UK.
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Zhou X, Chandrasekharan MB, Hall TC. High rooting frequency and functional analysis of GUS and GFP expression in transgenic Medicago truncatula A17. THE NEW PHYTOLOGIST 2004; 162:813-822. [PMID: 33873758 DOI: 10.1111/j.1469-8137.2004.01065.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
• An effective transformation method is described for Medicago truncatula A17, verifying its suitability as a model legume for functional genomics. • Media and culture methods are detailed that yielded an average frequency of 35% for recovery of transgenic shoots from cotyledonary node explants and 39% for root induction and regeneration of entire plants from 419 phosphinothricin-resistant shoots. • Fertile plants transgenic for both 35S-GFP and phas-GUS were obtained in five of eight independent experiments. The presence and stable inheritance of transgenes was confirmed by GFP or GUS expression and by genomic DNA blots. GFP expression driven by the normally constitutive CaMV 35S promoter diminished as the leaves matured. Although GUS was very strongly and uniformly expressed in seed cotyledons of most lines, one line exhibited an aberrant, patchy pattern. Additionally, weak GUS expression was evident in leaf veins from the normally stringently spatially regulated phas promoter. • Stably transformed, fertile, M. truncatula A17 plants were generated. The unconventional expression patterns for 35S-GFP and phas-GUS expression obtained in some transformants suggest the occurrence of novel epigenetic events.
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Affiliation(s)
- Xin Zhou
- Institute of Developmental and Molecular Biology and Department of Biology, Texas A & M University, College Station, TX 77843-3155, USA
| | - Mahesh B Chandrasekharan
- Institute of Developmental and Molecular Biology and Department of Biology, Texas A & M University, College Station, TX 77843-3155, USA
| | - Timothy C Hall
- Institute of Developmental and Molecular Biology and Department of Biology, Texas A & M University, College Station, TX 77843-3155, USA
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Michiels A, Van den Ende W, Tucker M, Van Riet L, Van Laere A. Extraction of high-quality genomic DNA from latex-containing plants. Anal Biochem 2003; 315:85-9. [PMID: 12672415 DOI: 10.1016/s0003-2697(02)00665-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The isolation of intact, high-molecular-mass genomic DNA is essential for many molecular biology applications including long PCR, endonuclease restriction digestion, Southern blot analysis, and genomic library construction. Many protocols are available for the extraction of DNA from plant material. However, for latex-containing Asteraceae (Cichorioideae) species, standard protocols and commercially available kits do not produce efficient yields of high-quality amplifiable DNA. A cetyltrimethylammonium bromide protocol has been optimized for isolation of genomic DNA from latex-containing plants. Key steps in the modified protocol are the use of etiolated leaf tissue for extraction and an overnight 25 degrees C isopropanol precipitation step. The purified DNA has excellent spectral qualities, is efficiently digested by restriction endonucleases, and is suitable for long-fragment PCR amplification.
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Affiliation(s)
- An Michiels
- Laboratory of Plant Development, Institute of Botany and Microbiology, K. U. Leuven, Belgium.
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