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PCR-based detection of single sequence variants from a natural collection of the non-model tree species European Aspen Populus tremula (L.) Cover

PCR-based detection of single sequence variants from a natural collection of the non-model tree species European Aspen Populus tremula (L.)

Open Access
|Jun 2017

References

  1. AREND, M., A. STINZING, C. WIND, K. LANGER, A. LATZ, P. ACHE, J. FROMM and R. HEDRICH (2005): Polarlocalised poplar K+ channel capable of controlling electrical properties of wood-forming cells. Planta 223: 140-148.10.1007/s00425-005-0122-y
  2. BHANGALE, T. R., M. STEPHENS and D. A. NICKERSON (2006): Automating resequencing-based detection of insertion-deletion polymorphisms. Nature Genetics 38: 1457-1462.10.1038/ng1925
  3. CARDON, L. R. and J. I. BELL (2001): Association study designs for complex diseases. Nature reviews. Genetics 2: 91-99.
  4. CSEKE, L. J., J. ZHENG and G. K. PODILA (2003): Characterization of PTM5 in aspen trees: a MADSbox gene expressed during woody vascular development. Gene 318: 55-67.10.1016/S0378-1119(03)00765-0
  5. DOYLE, J. J. and J. L. DOYLE (1987): A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19: 11-15.
  6. ECKENWALDER, J. E. (1996): Systematics and evolution of Populus, pp. 7-32. In: Biology of Populus and Its Implications for Management and Conservation, edited by R. F. STETTLER, N.R.C. Research Press, Ottawa, Canada.
  7. GARVIN, M. R., K. SAITOH and A. J. GHARRETT (2010): Application of single nucleotide polymorphisms to non-model species: a technical review. Molecular Ecology Resources 10: 915-934.10.1111/j.1755-0998.2010.02891.x21565101
  8. GOODSTEIN, D. M., S. SHU, R. HOWSON, R. NEUPANE, R. D. HAYES, J. FAZO, T. MITROS, W. DIRKS, U. HELLSTEN and N. PUTNAM (2012): Phytozome: a comparative platform for green plant genomics. Nucleic Acids Research: 1178-1186.10.1093/nar/gkr944324500122110026
  9. GRAY-MITSUMUNE, M., E. J. MELLEROWICZ, H. ABE, J. SCHRADER, A. WINZELL, F. STERKY, K. BLOMQVIST, S. MCQUEEN-MASON, T. T. TEERI and B. SUNDBERG (2004): Expansins abundant in secondary xylem belong to subgroup A of the alpha-expansin gene family. Plant Physiology 135: 1552-1564.10.1104/pp.104.03932151907015247397
  10. HAMANISHI, E. T., B. R. THOMAS and M. M. CAMPBELL (2012): Drought induces alterations in the stomatal development program in Populus. Journal of Experimental Botany 63: 4959-4971.10.1093/jxb/ers177342799122760471
  11. HELYAR, S. J., J. HEMMER-HANSEN, D. BEKKEVOLD, M. I. TAYLOR, R. OGDEN, M. T. LIMBORG, A. CARIANI, G. E. MAES, E. DIOPERE and G.. R. CARVALHO (2011): Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges. Molecular Ecology Resources 11: 123-136.10.1111/j.1755-0998.2010.02943.x21429169
  12. INGVARSSON, P. K. (2005): Nucleotide polymorphism and linkage disequilibrium within and among natural populations of European aspen (Populus tremula L., Salicaceae), Genetics 169: 945-953.10.1534/genetics.104.034959144910915489521
  13. INGVARSSON, P. K. (2008): Multilocus patterns of nucleotide polymorphism and the demographic history of Populus tremula. Genetics 180: 329-340.10.1534/genetics.108.090431253568518716330
  14. ISMAIL, M., R. Y. SOOLANAYAKANAHALLY, P. K. INGVARSSON, R. D. GUY, S. JANSSON, S. N. SILIM and Y. A. EL-KASSABY (2012): Comparative nucleotide diversity across North American and European populus species. Journal of Molecular Evolution 74: 257-272.10.1007/s00239-012-9504-5
  15. JOHANSSON, H., F. STERKY, B. AMINI, J. LUNDEBERG and L. A. KLECZKOWSKI (2002): Molecular cloning and characterization of a cDNA encoding poplar UDP-glucose dehydrogenase, a key gene of hemicellulose/pectin formation. Biochimica et Biophysica Acta 1576: 53-58.10.1016/S0167-4781(02)00292-0
  16. JOSEPH, J. A. and C. LEXER (2008): A set of novel DNA polymorphisms within candidate genes potentially involved in ecological divergence between Populus alba and P. tremula, two hybridizing European forest trees. Molecular Ecology Resources 8: 188-192.10.1111/j.1471-8286.2007.01919.x21585752
  17. KELLEHER, S. R., N. LEVSEN, M. S. OLSON and P. TIFFIN (2012): Local Adaptation in the Flowering-Time Gene Network of Balsam Poplar, Populus balsamifera L. Molecular Biology and Evolution 29: 3143-3152.10.1093/molbev/mss12122513286
  18. LANGER, K., P. ACHE, D. GEIGER, A. STINZING, M. AREND, C. WIND, S. REGAN, J. FROMM and R. HEDRICH (2002): Poplar potassium transporters capable of controlling K+ homeostasis and K+- dependent xylogenesis. The Plant journal: for cell and molecular biology 32: 997-1009.10.1046/j.1365-313X.2002.01487.x
  19. LEE, J. H., W. TERZAGHI, G. GUSMAROLI, J. B. CHARRON, H. J. YOON, H. CHEN, Y. J. HE, Y. XIONG and X.W. DENG (2008): Characterization of Arabidopsis and rice DWD proteins and their roles as substrate receptors for CUL4-RING E3 ubiquitin ligases. The Plant Cell 20: 152-167.10.1105/tpc.107.055418225492918223036
  20. LI, X., C. ZHU, C. T. YEH, W. WU, E. M. TAKACS, K. A. PETSCH, F. TIAN, G. BAI, E. S. BUCKLER, G. J. MUEHLBAUER et al. (2012): Genic and nongenic contributions to natural variation of quantitative traits in maize. Genome Research DOI 10.1101/gr.140277.11210.1101/gr.140277.112351467322701078
  21. LIU, K. and S. V. MUSE (2005): PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21: 2128-2129.10.1093/bioinformatics/bti28215705655
  22. MARJANOVIC, Z., N. UEHLEIN, R. KALDENHOFF, J. J. ZWIAZEK, M. WEISS, R. HAMPP and U. NEHLS (2005): Aquaporins in poplar: what a difference a symbiont makes!. Planta 222: 258-268.10.1007/s00425-005-1539-z15883833
  23. MASLE, J., S. R. GILMORE and G. D. FARQUHAR (2005): The ERECTA gene regulates plant transpiration efficiency in Arabidopsis. Nature 436: 866-870.10.1038/nature0383516007076
  24. NICKERSON, D. A., V. O. TOBE and S. L. TAYLOR (1997): PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing. Nucleic Acids Research 25: 2745-2751.10.1093/nar/25.14.27451468179207020
  25. OLSON, M. S., A. L. ROBERTSON, N. TAKEBAYASHI, S. SILIM, W. R. SCHROEDER and P. TIFFIN (2010): Nucleotide diversity and linkage disequilibrium in balsam poplar (Populus balsamifera). The New Phytologist 186: 526-536.10.1111/j.1469-8137.2009.03174.x20122131
  26. ROZEN, S. and H. SKALETSKY (2000): Primer3 on the WWW for general users and for biologist programmers. Methods in Molecular Biology 132: 365-386.
  27. SCHROEDER, H., A. M. HOELTKEN and M. FLADUNG (2012): Differentiation of Populus species using chloroplast single nucleotide polymorphism (SNP) markers - essential for comprehensible and reliable poplar breeding. Plant Biology 14: 374-381.10.1111/j.1438-8677.2011.00502.x21973311
  28. SEEB, L. W., W. D. TEMPLIN, S. SATO, S. ABE, K. WARHEIT, J. Y. PARK and J. E. SEEB (2011): Single nucleotide polymorphisms across a species’ range: implications for conservation studies of Pacific salmon. Molecular Ecology Resources 11 Suppl 1: 195-217.10.1111/j.1755-0998.2010.02966.x21429175
  29. SEIFERT, S., B. VORNAM and R. FINKELDEY (2012): DNA sequence variation and development of SNP markers in beech (Fagus sylvatica L.). European Journal of Forest Research 131: 1761-1770.10.1007/s10342-012-0630-9
  30. SLATE, J., J. GRATTEN, D. BERALDI, J. STAPLEY, M. HALE and J. M. PEMBERTON (2009): Gene mapping in the wild with SNPs: guidelines and future directions. Genetica 136: 97-107.10.1007/s10709-008-9317-z18780148
  31. STRAUSS, S. H. and F. M. MARTIN (2004): Poplar genomics comes of age. New Phytologist 164: 1-4.10.1111/j.1469-8137.2004.01179.x33873475
  32. STREET, N. R., O. SKOGSTROM, A. SJODIN, J. TUCKER, M. RODRIGUEZ-ACOSTA, P. NILSSON, S. JANSSON and G. TAYLOR (2006): The genetics and genomics of the drought response in Populus. Plant Journal 48: 321-341.10.1111/j.1365-313X.2006.02864.x17005011
  33. TUSKAN, G. A., S. DIFAZIO, S. JANSSON, J. BOHLMANN, I. GRIGORIEV, U. HELLSTEN, N. PUTNAM, S. RALPH, S. ROMBAUTS, A. SALAMOV et al. (2006): The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313: 1596-1604.10.1126/science.112869116973872
  34. VAHISALU, T., H. KOLLIST, Y. F. WANG, N. NISHIMURA, W. Y. CHAN, G. VALERIO, A. LAMMINMAKI, M. BROSCHE, H. MOLDAU and R. DESIKAN et al. (2008): SLAC1 is required for plant guard cell S-type anion channel function in stomatal signalling. Nature 452: 487-491.10.1038/nature06608285898218305484
  35. WANG, W. X., D. PELAH, T. ALERGAND, O. SHOSEYOV and A. ALTMAN (2002): Characterization of SP1, a stress-responsive, boiling-soluble, homo-oligomeric protein from aspen. Plant Physiology 130: 865-875.10.1104/pp.00243616661312376651
  36. WILKINS, O., L. WALDRON, H. NAHAL, N. J. PROVART and M. M. CAMPBELL (2009): Genotype and time of day shape the Populus drought response. The Plant Journal 60: 703-715.10.1111/j.1365-313X.2009.03993.x19682285
  37. WINKLER, S., N. GSCHEIDEL and M. BRAND (2011): Mutant generation in vertebrate model organisms by TILLING. Methods in Molecular Biology 770: 475-504.10.1007/978-1-61779-210-6_1921805277
  38. YOSHIURA, K., A. KINOSHITA, T. ISHIDA, A. NINOKATA, T. ISHIKAWA, T. KANAME, M. BANNAI, K. TOKUNAGA, S. SONODA and R. KOMAKI et al. (2006): A SNP in the ABCC11 gene is the determinant of human earwax type. Nature Genetics 38: 324-330.10.1038/ng173316444273
DOI: https://doi.org/10.1515/sg-2015-0024 | Journal eISSN: 2509-8934 | Journal ISSN: 0037-5349
Language: English
Page range: 259 - 269
Submitted on: Nov 11, 2015
Published on: Jun 7, 2017
Published by: Johann Heinrich von Thünen Institute
In partnership with: Paradigm Publishing Services
Publication frequency: 1 issue per year

© 2017 S. Winkler, K. Linke, N. Gscheidel, M. Meyer, Doris Krabel, published by Johann Heinrich von Thünen Institute
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.