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A Novel Set of Chloroplast SSR Markers for the Genus Juglans Reveals Within Species Differentiation Cover

A Novel Set of Chloroplast SSR Markers for the Genus Juglans Reveals Within Species Differentiation

Open Access
|Jul 2024

References

  1. Bai WN, Liao WJ, Zhang DY (2010) Nuclear and chloroplast DNA phylogeography reveal two refuge areas with asymmetrical gene flow in a temperate walnut tree from East Asia. New Phytologist, 188(3), 892-901. https://doi.org/10.1111/j.1469-8137.2010.03407.x
  2. Bernard A, Lheureux F, Dirlewanger E (2018) Walnut: past and future of genetic improvement. Tree genetics & genomes, 14(1), 1. https://doi.org/10.1007/s11295-017-1214-0
  3. Brownstein MJ, Carpten JD, Smith JR (1996) Modulation of Non-Templated Nucleotide Addition by Taq DNA Polymerase: Primer Modifications that Facilitate Genotyping. BioTechniques, 20(6), 1004–1010. https://doi.org/10.2144/96206st01
  4. Dangl GS, Woeste K, Aradhya MK, Koehmstedt A, Simon C, Potter D, Leslie CA, McGranahan G (2005) Characterization of 14 microsatellite markers for genetic analysis and cultivar identification of walnut. Journal of the American Society for Horticultural Science, 130(3), 348-354. https://doi.org/10.21273/jashs.130.3.348
  5. Dong W, Xu C, Li W, Xie X, Lu Y, Liu Y, Jin X, Suo Z (2017) Phylogenetic resolution in Juglans based on complete chloroplast genomes and nuclear DNA sequences. Front Plant Sci. Jun 30; 8:1148. https://doi.org/10.3389/fpls.2017.01148
  6. Ebrahimi A, Mathur S, Lawson SS, LaBonte NR, Lorch A, Coggeshall MV, Woeste KE (2019) Microsatellite borders and micro-sequence conservation in Juglans. Scientific Reports, 9(1), 3748. https://doi.org/10.1038/s41598-019-39793-z
  7. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Mol Ecol 14:2611–2620. https://doi.org/10.1111/j.1365-294X.2005.02553.x
  8. Götz J, Gailing O (2022) A novel set of polymorphic chloroplast microsatellite markers for northern red oak (Q. rubra L.). Plant Genetic Resources, 20(2), 174-177. https://doi.org/10.1017/S1479262122000156
  9. Götz J, Leinemann L, Gailing O, Hardtke A, Caré O (2024) Development of a highly polymorphic chloroplast SSR set in Abies grandis with transferability to other conifer species – A promising toolkit for gene flow investigations. Ecology and Evolution. https://doi.org/10.1002/ece3.11593
  10. Hu Y, Woeste KE, Zhao P (2017) Completion of the chloroplast genomes of five Chinese Juglans and their contribution to chloroplast phylogeny. Frontiers in Plant Science, 7, 231924. https://doi.org/10.3389/fpls.2016.01955
  11. Kopelman NM, Mayzel J, Jakobsson M, Rosenberg NA, Mayrose I (2015) Clump-ak: A program for identifying clustering modes and packaging population structure inferences across K. Mol Ecol Resour. 15:1179–1191. https://doi.org/10.1111/1755-0998.12387
  12. Li YL, Liu JX (2018) StructureSelector: A web based software to select and visualize the optimal number of clusters using multiple methods. Molecular Ecology Resources, 18:176–177. https://doi.org/10.1111/1755-0998.12719
  13. Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol. Ecol. Notes 6, 288–295. https://doi.org/10.1111/j.1471-8286.2005.01155.x
  14. Peng S, Yang G, Liu C, Yu Z, Zhai M (2017) The complete chloroplast genome of the Juglans regia (Juglandales: Julandaceae). Mitochondrial DNA Part A, 28(3), 407-408. https://doi.org/10.3109/19401736.2015.1127367
  15. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959. https://doi.org/10.1093/genetics/155.2.945
  16. Provan J, Powell W, Hollingsworth PM (2001) Chloroplast microsatellites: new tools for studies in plant ecology and evolution. Trends in Ecology & Evolution, 16(3), 142-147. https://doi.org/10.1016/S0169-5347(00)02097-8
  17. R Core Team R. (2013) R: A language and environment for statistical computing. Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nature Biotechnology, 18(2), 233-234. https://doi.org/10.1038/72708
  18. Souframanien J, Reddy KS (2015) De novo assembly, characterization of immature seed transcriptome and development of genic-SSR markers in black gram [Vigna mungo (L.) Hepper]. PLoS One, 10(6), e0128748. https://doi.org/10.1371/journal.pone.0128748
  19. Zhang R, Zhu A, Wang X, Yu J, Zhang H, Gao J, Cheng Y, Deng X (2010) Development of Juglans regia SSR markers by data mining of the EST database. Plant Molecular Biology Reporter, 28, 646-653. https://doi.org/10.1007/s11105-010-0192-2
  20. Zhao P, Zhou HJ, Potter D, Hu YH, Feng XJ, Dang M, Feng L, Zulfigar S, Liu W-Z, Zhao G-F,Woeste K (2018) Population genetics, phylogenomics and hybrid speciation of Juglans in China determined from whole chloroplast genomes, transcriptomes, and genotyping-by-sequencing (GBS). Molecular Phylogenetics and Evolution, 126, 250-265. https://doi.org/10.1016/j.ympev.2018.04.014
DOI: https://doi.org/10.2478/sg-2024-0012 | Journal eISSN: 2509-8934 | Journal ISSN: 0037-5349
Language: English
Page range: 120 - 125
Published on: Jul 22, 2024
Published by: Johann Heinrich von Thünen Institute
In partnership with: Paradigm Publishing Services
Publication frequency: 1 issue per year

© 2024 Jeremias Götz, Oliver Caré, Winston Beck, Oliver Gailing, Bernhard Hosius, Ludger Leinemann, published by Johann Heinrich von Thünen Institute
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.