1. bookVolume 71 (2022): Edition 1 (January 2022)
Détails du magazine
License
Format
Magazine
eISSN
2509-8934
Première parution
22 Feb 2016
Périodicité
1 fois par an
Langues
Anglais
access type Accès libre

Flexible DNA isolation procedure for different tree species as a convenient lab routine

Publié en ligne: 01 Jul 2022
Volume & Edition: Volume 71 (2022) - Edition 1 (January 2022)
Pages: 20 - 30
Détails du magazine
License
Format
Magazine
eISSN
2509-8934
Première parution
22 Feb 2016
Périodicité
1 fois par an
Langues
Anglais
Abstract

DNA isolation is a fundamental technique for all molecular biology laboratories. Depending on the plant species, DNA isolation can be challenging. In particular, adapted protocols rarely exist for tree species which are not used as standard model organisms. Here, we describe a flexible DNA isolation protocol that works for 59 tree species in a modular system. It is based on an ATMAB-containing extraction buffer to which proteinase K and/or boric acid are added, depending on the plant species. Subsequent purification steps include one or two precipitations with dichloromethane and, depending on the tree species, an optional sodium acetate precipitation. Using leaf material of a hybrid poplar clone from in vitro culture, it was determined that higher amounts of DNA could be isolated with this material than from field leaves. Starting from leaf material, DNA isolation for difficult cases was achieved with cambium or root tissue. This protocol was used to extract DNA for subsequent PCR amplification. Markers for cpDNA, mtDNA, and genomic DNA were used for standardized testing.

Álvarez I (2003) Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution 29(3):417–434. https://dx.doi.org/10.1016/S1055-7903(03)00208-210.1016/S1055-7903(03)00208-2 Search in Google Scholar

Baldwin BG (1992) Phylogenetic utility of the internal transcribed spacers of nuclear ribosomal DNA in plants: An example from the compositae. Molecular Phylogenetics and Evolution 1(1):3–16. https://dx.doi.org/10.1016/1055-7903(92)90030-K10.1016/1055-7903(92)90030-K Search in Google Scholar

Baldwin BG (1993) Molecular Phylogenetics of Calycadenia (Compositae) Based on ITS Sequences of Nuclear Ribosomal DNA: Chromosomal and Morphological Evolution Reexamined. American Journal of Botany 80(2):222. https://dx.doi.org/10.2307/244504310.2307/2445043 Search in Google Scholar

Barzegari A, Vahed SZ, Atashpaz S, Khani S, Omidi Y (2010) Rapid and simple methodology for isolation of high quality genomic DNA from coniferous tissues (Taxus baccata). Mol Biol Rep 37(2):833–837. https://dx.doi.org/10.1007/s11033-009-9634-z10.1007/s11033-009-9634-z19649730 Search in Google Scholar

Blanc-Jolivet C, Yanbaev Y, Kersten B, Degen B (2018) A set of SNP markers for timber tracking of Larix spp. in Europe and Russia. Forestry (Lond) 91(5):614–628. https://dx.doi.org/10.1093/forestry/cpy02010.1093/forestry/cpy020 Search in Google Scholar

Brenner WG, Mader M, Müller NA, Hoenicka H, Schroeder H, Zorn I, Fladung M, Kersten B (2019) High Level of Conservation of Mitochondrial RNA Editing Sites Among Four Populus Species. G3 (Bethesda, Md.) 9(3):709–717. https://dx.doi.org/10.1534/g3.118.20076310.1534/g3.118.200763640459530617214 Search in Google Scholar

Bruegmann T, Fladung M (2013) Potentials and limitations of the cross-species transfer of nuclear microsatellite marker in six species belonging to three sections of the genus Populus L. Tree Genetics & Genomes 9(6):1413–1421. https://dx.doi.org/10.1007/s11295-013-0647-310.1007/s11295-013-0647-3 Search in Google Scholar

Bruegmann T, Fladung M (2019) Overexpression of both flowering time genes AtSOC1 and SaFUL revealed huge influence onto plant habitus in poplar 15(2):1–13. https://dx.doi.org/10.1007/S11295-019-1326-910.1007/s11295-019-1326-9 Search in Google Scholar

Bruegmann T, Deecke K, Fladung M (2019) Evaluating the Efficiency of gRNAs in CRISPR/Cas9 Mediated Genome Editing in Poplars. International journal of molecular sciences 20(15). https://dx.doi.org/10.3390/ijms2015362310.3390/ijms20153623669623131344908 Search in Google Scholar

Colpaert N, Cavers S, Bandou E, Caron H, Gheysen G, Lowe AJ (2005) Sampling Tissue for DNA Analysis of Trees: Trunk Cambium as an Alternative to Canopy Leaves. Silvae Genetica 541-6:265–269. https://dx.doi.org/10.1515/sg-2005-003810.1515/sg-2005-0038 Search in Google Scholar

Degen B, Yanbaev Y, Mader M, Ianbaev R, Bakhtina S, Schroeder H, Blanc-Jolivet C (2021) Impact of Gene Flow and Introgression on the Range Wide Genetic Structure of Quercus robur (L.) in Europe. Forests 12(10):1425. https://dx.doi.org/10.3390/f1210142510.3390/f12101425 Search in Google Scholar

Doyle JJ, Doyle JL (1990) Isolation of Plant DNA from Fresh Tissue. Focus 12(13):39–40 Search in Google Scholar

Dumolin S, Demesure B, Petit RJ (1995) Inheritance of chloroplast and mitochondrial genomes in pedunculate oak investigated with an efficient PCR method. Theor Appl Genet 91:1253–1256. https://dx.doi.org/10.1007/BF0022093710.1007/BF0022093724170054 Search in Google Scholar

Fladung M, Schroeder H, Wehenkel C, Kersten B (2015) Differentiation of six Eucalyptus trees grown in Mexico by ITS and six chloroplast barcoding markers. Silvae Genetica 641-6:121–130. https://dx.doi.org/10.1515/sg-2015-001210.1515/sg-2015-0012 Search in Google Scholar

Janabi AHD, Kerkhof LJ, McGuinness LR, Biddle AS, McKeever KH (2016) Comparison of a modified phenol/chloroform and commercial-kit methods for extracting DNA from horse fecal material. Journal of Microbiological Methods 129:14–19. https://dx.doi.org/10.1016/j.mimet.2016.07.01910.1016/j.mimet.2016.07.01927460337 Search in Google Scholar

Köchl S, Niederstätter H, Parson W (2005) DNA Extraction and Quantitation of Forensic Samples Using the Phenol–Chloroform Method and Real-Time PCR. In: Carracedo A. (Hrsg) Forensic DNA Typing Protocols. Methods in Molecular Biology. Humana Press, New Jersey, S 13–30. https://dx.doi.org/10.1385/1-59259-867-6:01310.1385/1-59259-867-6:013 Search in Google Scholar

Leple JC, Brasileiro AC, Michel MF, Delmotte F, Jouanin L (1992) Transgenic poplars: expression of chimeric genes using four different constructs. Plant cell reports 11(3):137–141. https://dx.doi.org/10.1007/BF0023216610.1007/BF0023216624213546 Search in Google Scholar

Mader M, Schroeder H, Schott T, Schöning-Stierand K, Leite Montalvão AP, Liesebach H, Liesebach M, Fussi B, Kersten B (2020) Mitochondrial Genome of Fagus sylvatica L. as a Source for Taxonomic Marker Development in the Fagales. Plants 9(10):1274. https://dx.doi.org/10.3390/plants910127410.3390/plants9101274765081432992588 Search in Google Scholar

Müller NA, Kersten B, Leite Montalvão AP, Mähler N, Bernhardsson C, Bräutigam K, Carracedo Lorenzo Z, Hoenicka H, Kumar V, Mader M, Pakull B, Robinson KM, Sabatti M, Vettori C, Ingvarsson PK, Cronk Q, Street NR, Fladung M (2020) A single gene underlies the dynamic evolution of poplar sex determination. Nature plants 6(6):630–637. https://dx.doi.org/10.1038/s41477-020-0672-910.1038/s41477-020-0672-932483326 Search in Google Scholar

Renshaw MA, Olds BP, Jerde CL, McVeigh MM, Lodge DM (2015) The room temperature preservation of filtered environmental DNA samples and assimilation into a phenol-chloroform-isoamyl alcohol DNA extraction. Mol Ecol Re-sour 15(1):168–176. https://dx.doi.org/10.1111/1755-0998.1228110.1111/1755-0998.12281431248224834966 Search in Google Scholar

Sambrook J, Fritsch E, Maniatis T (1989) Molecular cloning; A laboratory manual. Second edition. Cold Spring Harbor, New York Search in Google Scholar

Schott T, Schroeder H, Schöning-Stierand K, Kersten B (2019) The complete chloroplast genome sequence of Pinus cembra L. (Pinaceae). Mitochondrial DNA. Part B, Resources 4(2):4202–4203. https://dx.doi.org/10.1080/23802359.2019.169329710.1080/23802359.2019.1693297770774733366383 Search in Google Scholar

Schröder H, Yanbaev Y, Kersten B, Degen B (2019) Short note: Development of a new set of SNP markers to measure genetic diversity and genetic differentiation of Mongolian oak (Quercus mongolica Fisch. ex Ledeb.) in the Far East of Russia. Silvae Genetica 68(1):85–91. https://dx.doi.org/10.2478/sg-2019-001610.2478/sg-2019-0016 Search in Google Scholar

Schroeder H, Hoeltken AM, Fladung M (2012) Differentiation of Populus species using chloroplast single nucleotide polymorphism (SNP) markers--essential for comprehensible and reliable poplar breeding. Plant Biology 14(2):374–381. https://dx.doi.org/10.1111/j.1438-8677.2011.00502.x10.1111/j.1438-8677.2011.00502.x21973311 Search in Google Scholar

Schroeder H, Cronn R, Yanbaev Y, Jennings T, Mader M, Degen B, Kersten B (2016) Development of Molecular Markers for Determining Continental Origin of Wood from White Oaks (Quercus L. sect. Quercus). PloS one 11(6). https://dx.doi.org/10.1371/journal.pone.015822110.1371/journal.pone.0158221492482927352242 Search in Google Scholar

Schroeder H, Kersten B, Fladung M (2017) Development of Multiplexed Marker Sets to Identify the Most Relevant Poplar Species for Breeding. Forests 8(12):492. https://dx.doi.org/10.3390/f812049210.3390/f8120492 Search in Google Scholar

Souza HAV, Muller LAC, Brandão RL, Lovato MB (2012) Isolation of high quality and polysaccharide-free DNA from leaves of Dimorphandra mollis (Leguminosae), a tree from the Brazilian Cerrado. Genetics and molecular research : GMR 11(1):756–764. https://dx.doi.org/10.4238/2012.March.22.610.4238/2012.March.22.622576834 Search in Google Scholar

Articles recommandés par Trend MD

Planifiez votre conférence à distance avec Sciendo