Open Access

Identification of SNPs in candidate genes potentially involved in bud burst in European beech (Fagus sylvatica L.)


Cite

ALBERTO, F. J., J. DERORY, C. BOURY, J.-M. FRIGERIO, N. E. ZIMMERMANN and A. KREMER (2013): Imprints of natural selection along environmental gradients in phenology-related genes of Quercus petraea. Genetics 195: 495-512.10.1534/genetics.113.153783378197623934884Search in Google Scholar

BALDING, D. J. (2006): A tutorial on statistical methods for population association studies. Nature Reviews Genetics 7: 781-791.10.1038/nrg191616983374Search in Google Scholar

BASLER, D. and C. KÖRNER (2012): Photoperiod sensitivity of bud burst in 14 temperate forest tree species. Agricultural and Forest Meteorology 165: 73-81.10.1016/j.agrformet.2012.06.001Search in Google Scholar

BERTIN, R. I. (2008): Plant phenology and distribution in relation to recent climate change. The Journal of the Torrey Botanical Society 135: 126-146.10.3159/07-RP-035R.1Search in Google Scholar

BOLTE, A., T. CZAJKOWSKI and T. KOMPA (2007): The north-eastern distribution range of European beech - a review. Forestry 80: 413-429.10.1093/forestry/cpm028Search in Google Scholar

CAFFARRA, A. and A. DONNELLY (2011): The ecological significance of phenology in four different tree species: effects of light and temperature on bud burst. International Journal of Biometeorology 55: 711-721.10.1007/s00484-010-0386-121113629Search in Google Scholar

CARSJENS, C., Q. N. NGUYEN, J. GUZY, F. KNUTZEN, I. C. MEIER, M. MÜLLER, R. FINKELDEY, C. LEUSCHNER and A. POLLE (2014): Intra-specific variations of stress-related genes in beech progenies are stronger than drought-induced responses. Tree Physiology 34: 1348-1361.10.1093/treephys/tpu09325430883Search in Google Scholar

DERORY, J., P. LÉGER, V. GARCIA, J. SCHAEFFER, M.-T. HAUSER, F. SALIN, C. LUSCHNIG, C. PLOMION, J. GLÖSSL and A. KREMER (2006): Transcriptome analysis of bud burst in sessile oak (Quercus petraea). New Phytologist 170: 723-738.10.1111/j.1469-8137.2006.01721.x16684234Search in Google Scholar

DITTMAR, C., W. FRICKE and W. ELLING (2006): Impact of late frost events on radial growth of common beech (Fagus sylvatica L.) in Southern Germany. European Journal of Forest Research 125: 249-259.10.1007/s10342-005-0098-ySearch in Google Scholar

EUROPEAN ENVIRONMENT AGENCY (EEA) (2012): Climate change, impact and vulnerability in Europe 2012, an indicator-based report. European Environment Agency, Copenhagen.Search in Google Scholar

FISCHER, M., O. BOSSDORF, S. GOCKEL, F. HÄNSEL, A. HEMP, D. HESSENMÖLLER, G. KORTE, J. NIESCHULZE, S. PFEIFFER, D. PRATI, S. RENNER, I. SCHÖNING, U. SCHUMACHER, K. WELLS, F. BUSCOT, E. K. V. KALKO, K. E. LINSENMAIR, E.-D. SCHULZE and W. W. WEISSER (2010): Implementing largescale and long-term functional biodiversity research: The Biodiversity Exploratories. Basic and Applied Ecology 11: 473-485.10.1016/j.baae.2010.07.009Search in Google Scholar

GÖMÖRY, D., L. PAULE, I. M. SHVADCHAK, F. POPESCU, M. SULKOWSKA, V. HYNEK and R. LONGAUER (2003): Spatial patterns of the genetic differentiation in European beech (Fagus sylvatica L.) at allozyme loci in the Carpathians and the adjacent regions. Silvae Genetica 52: 78-83.Search in Google Scholar

GRIFFITHS, S., R. P. DUNFORD, G. COUPLAND and D. A. LAURIE (2003): The evolution of CONSTANS-Like gene families in barley, rice and Arabidopsis. Plant Physiology 131: 1855-1867.10.1104/pp.102.01618816694212692345Search in Google Scholar

GU, L., P. J. HANSON, W. M. POST, D. P. KAISER, B. YANG, R. NEMANI, S. G. PALLARDY and T. MEYERS (2008): The 2007 eastern US spring freeze: increasing cold damage in a warming world. BioScience 58: 253-262.10.1641/B580311Search in Google Scholar

HALL, T. A. (1999): BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41: 95-98.Search in Google Scholar

HELYAR, S. J., J. HEMMER-HANSEN, D. BEKKEVOLD, M. I. TAYLOR, R. OGDEN, M. T. LIMBORG, A. CARIANI, G. E. MAES, E. DIOPERE, G. R. CARVALHO and E. E. NIELSEN (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.x21429169Search in Google Scholar

HEMMER-HANSEN, J., E. E. G. NIELSEN, D. MELDRUP and C. Mittelholzer (2011): Identification of single nucleotide polymorphisms in candidate genes for growth and reproduction in a nonmodel organism; the Atlantic cod, Gadus morhua. Molecular Ecology Resources 11: 71-80.10.1111/j.1755-0998.2010.02940.x21429164Search in Google Scholar

HERTEL, D., T. STRECKER, H. MÜLLER-HAUBOLD and C. LEUSCHNER (2013): Fine root biomass and dynamics in beech forests across a precipitation gradient - is optimal resource partitioning theory applicable to water-limited mature trees? Journal of Ecology 101: 1183-1200.10.1111/1365-2745.12124Search in Google Scholar

HEUERTZ, M., E. DE PAOLI, T. KÄLLMAN, H. LARSSON, I. JURMAN, M. MORGANTE, M. LASCOUX and N. GYLLENSTRAND (2006): Multilocus patterns of nucleotide diversity, linkage disequilibrium and demographic history of Norway spruce [Picea abies (L.) Karst]. Genetics 174: 2095-2105.10.1534/genetics.106.065102169865617057229Search in Google Scholar

HILL, W. G. and A. ROBERTSON (1968): Linkage disequilibrium in finite populations. Theoretical and Applied Genetics 38: 226-231.10.1007/BF0124562224442307Search in Google Scholar

HORVATH, D. (2009): Common mechanisms regulate flowering and dormancy. Plant Science 177: 523-531.10.1016/j.plantsci.2009.09.002Search in Google Scholar

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.104.034959144910915489521Search in Google Scholar

INGVARSSON, P. K., M. V. GARCIA, V. LUQUEZ, D. HALL and S. JANSSON (2008): Nucleotide polymorphism and phenotypic associations within and around the phytochrome B2 locus in European aspen (Populus tremula, Salicaceae). Genetics 178: 2217-2226.10.1534/genetics.107.082354232381018245834Search in Google Scholar

KHANDURI, V. P., C. M. SHARMA and S. P. SINGH (2008): The effects of climate change on plant phenology. Environmentalist 28: 143-147.10.1007/s10669-007-9153-1Search in Google Scholar

KIBBE, W. A. (2007): OligoCalc: an online oligonucleotide properties calculator. Nucleic Acids Research 35: W43-W46.10.1093/nar/gkm234193319817452344Search in Google Scholar

KÖRNER, C. and D. BASLER (2010): Phenology under global warming. Science 327: 1461-1462.10.1126/science.118647320299580Search in Google Scholar

KREYLING, J., D. THIEL, L. NAGY, A. JENTSCH, G. HUBER, M. KONNERT and C. BEIERKUHNLEIN (2012): Late frost sensitivity of juvenile Fagus sylvatica L. differs between southern Germany and Bulgaria and depends on preceding air temperature. European Journal of Forest Research 131: 717-725.10.1007/s10342-011-0544-ySearch in Google Scholar

KRUTOVSKY, K. V. and D. B. NEALE (2005): Nucleotide diversity and linkage disequilibrium in cold-hardi- ness- and wood quality-related candidate genes in Douglas fir. Genetics 171: 2029-2041.10.1534/genetics.105.044420145612316157674Search in Google Scholar

LALAGÜE, H., K. CSILLÉRY, S. ODDOU-MURATORIO, J. SAFRANA, C. DE QUATTRO, F. FADY, S. C. GONZÁLEZ-MARTÍNEZ and G. G. VENDRAMIN (2014): Nucleotide diversity and linkage disequilibrium at 58 stress response and phenology candidate genes in a European beech (Fagus sylvatica L.) population from southeastern France. Tree Genetics and Genomes 10: 15-26.10.1007/s11295-013-0658-0Search in Google Scholar

LARSSON, H., T. KÄLLMAN, N. GYLLENSTRAND and M. LASCOUX (2013): Distribution of long-range linkage disequilibrium and Tajima’s D values in Scandinavian Populations of Norway Spruce (Picea abies). G3: Genes, Genomes, Genetics 3: 795-806.10.1534/g3.112.005462365672723550126Search in Google Scholar

LIBRADO, P. and J. ROZAS (2009): DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452.10.1093/bioinformatics/btp18719346325Search in Google Scholar

LIND-RIEHL, J. F., A. R. SULLIVAN and O. GAILING (2014): Evidence for selection on a Constans-like gene between two red oak species. Annals of Botany 113: 967-975.10.1093/aob/mcu019399763724615344Search in Google Scholar

MANLY, B. F. J. (1985): The statistics of natural selection on animal populations. Chapman & Hall, London.10.1007/978-94-009-4840-2Search in Google Scholar

MARCHLER-BAUER, A., M. K. DERBYSHIRE, N. R. GONZALES, S. LU, F. CHITSAZ, L. Y. GEER, R. C. GEER, J. HE, M. GWADZ, D. I. HURWITZ, C. J. LANCZYCKI, F. LU, G. H. MARCHLER, J. S. SONG, N. THANKI, Z. WANG, R. A. YAMASHITA, D. ZHANG, C. ZHENG and S. H. BRYANT (2015): CDD: NCBI’s conserved domain database. Nucleic Acids Research 43: D222-D226.10.1093/nar/gku1221438399225414356Search in Google Scholar

MARCHLER-BAUER, A. and S. H. BRYANT (2004): CDSearch: protein domain annotations on the fly. Nucleic Acids Research 32: W327-W331. MENZEL, A. and P. FABIAN (1999): Growing season extended in Europe. Nature 397: 659.Search in Google Scholar

MENZEL, A. (2000): Trends in phenological phases in Europe between 1951 and 1996. International Journal of Biometeorology 44: 76-81.10.1007/s00484000005410993561Search in Google Scholar

MORIN, P. A., G. LUIKART, R. K. WAYNE and THE SNP WORKSHOP GROUP (2004): SNPs in ecology, evolution and conservation. Trends in Ecology and Evolution 19: 208-216.10.1016/j.tree.2004.01.009Search in Google Scholar

NIELSEN, R. (2000): Estimation of population parameters and recombination rates from single nucleotide polymorphisms. Genetics 154: 931-942.10.1093/genetics/154.2.931146095410655242Search in Google Scholar

NIELSEN, R., M. J. HUBISZ and A. G. CLARK (2004): Reconstituting the frequency spectrum of ascertained single-nucleotide polymorphism data. Genetics 168: 2373-2382.10.1534/genetics.104.031039144875115371362Search in Google Scholar

PEAKALL, R. and P. E. SMOUSE (2006): GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6: 288-295.10.1111/j.1471-8286.2005.01155.xSearch in Google Scholar

PEAKALL, R. and P. E. SMOUSE (2012): GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28: 2537-2539.10.1093/bioinformatics/bts460346324522820204Search in Google Scholar

RAJENDRA, K. C., S. SEIFERT, K. PRINZ, O. GAILING and R. FINKELDEY (2014): Subtle human impacts on neutral genetic variation in European beech (Fagus sylvatica). Forest Ecology and Management 319: 138-149.10.1016/j.foreco.2014.02.003Search in Google Scholar

ROTZEN, S. and H. J. SKALETSKY (2000): Primer3 on the WWW for general users and for biologist programmers. In: KRAWETZ, S. and MISENER, S. (eds.) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, NJ, pp 365-386.Search in Google Scholar

ROUSSET, F. (2008): GENEPOP’007: a complete reimplementation of the GENEPOP software for Windows and Linux. Molecular Ecology Resources 8: 103-106.10.1111/j.1471-8286.2007.01931.x21585727Search in Google Scholar

SAMBROOK, J., E. F. FISCHER and T. MANIATIS (1989): Molecular cloning: a laboratory manual. 2nd ed. Cold Spring Harbor N.Y., Cold Spring Harbor Laboratory.Search in Google Scholar

SEIFERT, S. (2012): Variation of candidate genes related to climate change in European beech (Fagus sylvatica L.). Dissertation. Georg-August- University Göttingen.Search in Google Scholar

SEIFERT, S., B. VORNAM and R. FINKELDEY (2012a): A set of 17 single nucleotide polymorphism (SNP) markers for European beech (Fagus sylvatica L.). Conservation Genetics Resources 4: 1045-1047.10.1007/s12686-012-9703-9Search in Google Scholar

SEIFERT, S., B. VORNAM and R. FINKELDEY (2012b): DNA sequence variation and development of SNP markers in beech (Fagus sylvatica L.). European Journal of Forest Research 131: 1761-1770.10.1007/s10342-012-0630-9Search in Google Scholar

TAJIMA, F. (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.10.1093/genetics/123.3.58512038312513255Search in Google Scholar

THOMPSON, J. D., D. G. HIGGINS and T. J. GIBSON (1994): CLUSTAL W: improving the sensitivity of progressive multiple sequence weighting, positionspecific gap penalties and weight matrix choice. Nucleic Acids Research 22: 4673-4680.10.1093/nar/22.22.46733085177984417Search in Google Scholar

UENO, S., G. LE PROVOST, V. LÉGER, C. KLOPP, C. NOIROT, J.-M. FRIGERIO, F. SALIN, J. SALSE, M. ABROUK, F. MURAT, O. BRENDEL, J. DERORY, P. ABADIE, P. LÉGER, C. CABANE, A. BARRÉ, A. DE DARUVAR, A. COULOUX, P. WINCKER, M.-P. REVIRON, A. KREMER and C. PLOMION (2010): Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak. BMC Genomics 11: 650.10.1186/1471-2164-11-650301786421092232Search in Google Scholar

VIDALIS, A., A. L. CURTU and R. FINKELDEY (2013): Novel SNP development and analysis at a NADP+- specific IDH enzyme gene in a four species mixed oak forest. Plant Biology 15: 126-137.10.1111/j.1438-8677.2012.00575.x22612737Search in Google Scholar

VIŠNJIĆ, Ć. and A. DOHRENBUSCH (2004): Frost - resistenz und Phänologie europäischer Buchenprovenienzen (Fagus sylvatica L.) Allgemeine Forst- und Jagdzeitung 175: 101-108.Search in Google Scholar

VOLLMER, N. L. and P. E. ROSEL (2012): Developing genomic resources for the common bottlenose dolphin (Tursiops truncatus): isolation and characterization of 153 single nucleotide polymorphisms and 53 genotyping assays. Molecular Ecology Resources 12: 1124-1132.10.1111/1755-0998.1200822978635Search in Google Scholar

VORNAM, B., O. GAILING, R. FINKELDEY, C. COLLADA, M. Á. GUEVERA, Á. SOTO, N. DE MARÍA, S. GONZÁLES-MARTÍNEZ, L. DÍAZ, R. ALIA, I. ARANDA, J. CLIMENT, M. T. CERVERA, P. GOICOECHEA, V. LÉGER, E. EVENO, J. DERORY, P. GARNIER-GÉRÉ, A. KREMER and C. PLOMION (2007): Naturally occurring nucleotide diversity in candidate genes for forest tree adaptation: magnitude, distribution and association with quantitative trait variation. GABI - The German Plant Genome Research Program, Progress report 2004-2007, pp 116-119.Search in Google Scholar

WÜHLISCH, GV., D. KRUSCHE and H.-J. MUHS (1995): Variation in temperature sum requirement for flushing of beech provenances. Silvae Genetica 44: 343-346.Search in Google Scholar

YAKOVLEV, I. A., C.-G. FOSSDAL Ø. JOHNSEN, O. JUNTTILA and T. SKØPPA (2006): Analysis of gene expression during bud burst initiation in Norway spruce via ESTs from subtracted cDNA libraries. Tree Genetics and Genomes 2: 39-52.10.1007/s11295-005-0031-zSearch in Google Scholar

YEH, F. C., R.-C. YANG and T. BOYLE (1999): POPGENE: Microsoft Windows-based freeware for population genetic analysis. University of Alberta, Canada (http://www.ualberta.ca/~fyeh/popgene.html)Search in Google Scholar

ZHANG, K. and L. JIN (2003): HaploBlockFinder: haplotype block analyses. Bioinformatics 19: 1300-1301.10.1093/bioinformatics/btg14212835279Search in Google Scholar

ZHU, M. and S. ZHAO (2007): Candidate gene identification approach: progress and challenges. International Journal of Biological Sciences 3: 420-427.10.7150/ijbs.3.420204316617998950Search in Google Scholar

eISSN:
2509-8934
Language:
English
Publication timeframe:
Volume Open
Journal Subjects:
Life Sciences, Molecular Biology, Genetics, Biotechnology, Plant Science