Geographical and environmental gradients shape phenotypic trait variation and genetic structure in Populus trichocarpa

. 2014 Mar ; 201 (4) : 1263-1276. [epub] 20131125

Jazyk angličtina Země Velká Británie, Anglie Médium print-electronic

Typ dokumentu časopisecké články, práce podpořená grantem, Research Support, U.S. Gov't, Non-P.H.S.

Perzistentní odkaz   https://www.medvik.cz/link/pmid24491114

• Populus trichocarpa is widespread across western North America spanning extensive variation in photoperiod, growing season and climate. We investigated trait variation in P. trichocarpa using over 2000 trees from a common garden at Vancouver, Canada, representing replicate plantings of 461 genotypes originating from 136 provenance localities. • We measured 40 traits encompassing phenological events, biomass accumulation, growth rates, and leaf, isotope and gas exchange-based ecophysiology traits. With replicated plantings and 29,354 single nucleotide polymorphisms (SNPs) from 3518 genes, we estimated both broad-sense trait heritability (H(2)) and overall population genetic structure from principal component analysis. • Populus trichocarpa had high phenotypic variation and moderate/high H(2) for many traits. H(2) ranged from 0.3 to 0.9 in phenology, 0.3 to 0.8 in biomass and 0.1 to 0.8 in ecophysiology traits. Most traits correlated strongly with latitude, maximum daylength and temperature of tree origin, but not necessarily with elevation, precipitation or heat : moisture indices. Trait H(2) values reflected trait correlation strength with geoclimate variables. The population genetic structure had one significant principal component (PC1) which correlated with daylength and showed enrichment for genes relating to circadian rhythm and photoperiod. • Robust relationships between traits, population structure and geoclimate in P. trichocarpa reflect patterns which suggest that range-wide geographical and environment gradients have shaped its genotypic and phenotypic variability.

Zobrazit více v PubMed

Benowicz A, Guy RD, El-Kassaby YA. 2000. Geographic pattern of genetic variation in photosynthetic capacity and growth in two hardwood species from British Columbia. Oecologia 123: 168-174.

Bradshaw HD Jr, Stettler RF. 1995. Molecular genetics of growth and development in Populus. IV. Mapping QTLs with large effects on growth, form, and phenology traits in a forest tree. Genetics 139: 963-973.

Burnham KP, Anderson DR. 2002. Model selection and multimodel inference: a practical information-theoretic approach, 2nd edn. New York, NY, USA: Springer.

Chamaillard S, Fichot R, Vincent-Barbaroux C, Bastien C, Depierreux C, Dreyer E, Villar M, Brignolas F. 2011. Variations in bulk leaf carbon isotope discrimination, growth and related leaf traits among three Populus nigra L. populations. Tree Physiology 31: 1076-1087.

Cooke JEK, Eriksson ME, Junttila O. 2012. The dynamic nature of bud dormancy in trees: environmental control and molecular mechanisms. Plant, Cell & Environment 35: 1707-1728.

Cronk QCB. 2005. Plant eco-devo: the potential of poplar as a model organism. New Phytologist 166: 39-48.

De Frenne P, Graae BJ, Rodríguez-Sánchez F, Kolb A, Chabrerie O, Decocq G, De Kort H, De Schrijver A, Diekmann M, Eriksson O et al. 2013. Latitudinal gradients as natural laboratories to infer species' responses to temperature. Journal of Ecology 101: 784-795.

Dutkowski GW, Costa e Silva J, Gilmour AR, Wellendorf H, Aguiar A. 2006. Spatial analysis enhances modeling of a wide variety of trials in forest genetic trials. Canadian Journal of Forest Research 36: 1851-1870.

Eckert AJ, Bower AD, Wegrzyn JL, Pande B, Jermstad KD, Krutovsky KV, St. Clair JB, Neale DB. 2009. Association genetics of coastal Douglas fir (Pseudotsuga menziesii var. menziesii, Pinaceae). I. Cold-hardiness related traits. Genetics 182: 1289-1302.

Eckert AJ, Dyer RJ. 2012. Defining the landscape of adaptive genetic diversity. Molecular Ecology 21: 2836-2838.

Fabbrini F, Gaudet M, Bastien C, Zaina G, Harfouche A, Beritognolo I, Marron N, Morgante M, Scarascia-Mugnozza G, Sabatti M. 2012. Phenotypic plasticity, QTL mapping and genomic characterization of bud set in black poplar. BMC Plant Biology 12: 47.

Farmer RE Jr. 1996. The genecology of Populus. In: Stettler RF, Bradshaw HD Jr, Heilman PE, Hinckley TM, eds. Biology of Populus and its implications for management and conservation. Ottawa, ON, Canada: NRC Research Press, 33-55.

Farrar JL. 1995. Trees in Canada. Ottawa, ON, Canada: Natural Resources Canada & Fitzhenry and Whiteside Limited.

Forsythe WC, Rykiel EJ Jr, Stahl RS, Wu H, Schoolfield RM. 1995. A model comparison for daylength as a function of latitude and day of year. Ecological Modelling 80: 87-95.

Fournier-Level A, Korte A, Cooper MD, Nordborg M, Schmitt J, Wilczek AM. 2011. A map of local adaptation in Arabidopsis thaliana. Science 334: 86-89.

Geraldes A, DiFazio SP, Slavov GT, Ranjan P, Muchero W, Hannemann J, Gunter LE, Wymore AM, Grassa CJ, Farzaneh N et al. 2013. A 34K SNP genotyping array for Populus trichocarpa: design, application to the study of natural populations and transferability to other Populus species. Molecular Ecology Resources 13: 306-323.

Geraldes A, Pang J, Thiessen N, Cezard T, Moore R, Zhao Y, Tam A, Wang S, Friedmann M, Birol I et al. 2011. SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing. Molecular Ecology Resources 11: 81-92.

Gilmour AR, Gogel BJ, Cullis BR, Welham SJ, Thompson R. 2002. ASReml user guide release 1.0. Hemel Hempstead, UK: VSN International Ltd.

Gornall JL, Guy RD. 2007. Geographic variation in ecophysiological traits of black cottonwood (Populus trichocarpa). Canadian Journal of Botany 85: 1202-1213.

Graffelman J, Morales J. 2008. Graphical test for Hardy-Weinberg equilibrium based on the temporary plot. Human Heredity 65: 77-84.

Guerra FP, Wegrzyn JL, Sykes R, Davis MF, Stanton BJ, Neale DB. 2013. Association genetics of chemical wood properties in black poplar (Populus nigra). New Phytologist 197: 162-176.

Hemani G, Knott S, Haley C. 2013. An evolutionary perspective on epistasis and the missing heritability. PLoS Genetics 9: e1003295.

Holliday JA, Ralph SG, White R, Bohlmann J, Aitken SN. 2008. Global monitoring of autumn gene expression within and among phenotypically divergent populations of Sitka spruce (Picea sitchensis). New Phytologist 178: 103-122.

Houlton BZ, Sigman DM, Schuur EAG, Hedin LO. 2007. A climate driven switch in plant nitrogen acquisition within tropical forest communities. Proceedings of the National Academy of Sciences, USA 104: 8902-8906.

Howe GT, Saruul P, Davis J, Chen THH. 2000. Quantitative genetics of bud phenology, frost damage, and winter survival in an F2 family of hybrid poplars. TAG. Theoretical and Applied Genetics. 101: 632-642.

Huang W, Pérez-García P, Pokhilko A, Millar AJ, Antoshechkin I, Riechmann JL, Mas P. 2012. Mapping the core of the Arabidopsis circadian clock defines the network structure of the oscillator. Science 336: 75-79.

Hudson ME, Lisch DR, Quail PH. 2003. The FHY3 and FAR1 genes encode transposase-related proteins involved in regulation of gene expression by the phytochrome A-signaling pathway. Plant Journal 34: 453-471.

Ibáñez C, Kozarewa I, Johansson M, Ögren E, Rohde A, Eriksson ME. 2010. Circadian clock components regulate entry and affect exit of seasonal dormancy as well as winter hardiness in Populus trees. Plant Physiology 153: 1823-1833.

Ingvarsson PK, Garcia MV, Luquez V, Hall D, Jansson S. 2008. Nucleotide polymorphism and phenotypic associations within and around the phytochrome B2 locus in European aspen (Populus tremula, Salicaceae). Genetics 178: 2217-2226.

Ingvarsson PK, Street NR. 2011. Association genetics of complex traits in plants. New Phytologist 189: 909-922.

Jackson DA. 1993. Stopping rules in Principal Components Analysis: a comparison of heuristical and statistical approaches. Ecology 74: 2204-2214.

Jansson S, Douglas CJ. 2007. Populus: a model system for plant biology. Annual Review of Plant Biology 58: 435-458.

Kawecki TJ, Ebert D. 2004. Conceptual issues in local adaptation. Ecology Letters 7: 1225-1241.

Keller SR, Levsen N, Olson MS, Tiffin P. 2012. Local adaptation in the flowering-time gene network of balsam poplar, Populus balsamifera L. Molecular Biology and Evolution 29: 3143-3152.

Keller SR, Soolanayakanahally RY, Guy RD, Silim SN, Olson MS, Tiffin P. 2011. Climate driven local adaptation of ecophysiology and phenology in balsam poplar Populus balsamifera L. (Salicaceae). American Journal of Botany 98: 99-108.

Lasky JR, Sun I-F, Su S-H, Chen Z-S, Keitt TH. 2013. Trait-mediated effects of environmental filtering on tree community dynamics. Journal of Ecology 101: 722-733.

Le Corre V, Kremer A. 2012. The genetic differentiation at quantitative trait loci under local adaptation. Molecular Ecology 21: 1548-1566.

Lexer C, Mangili S, Bossolini E, Forest F, Stölting KN, Pearman PB, Zimmermann NE, Salamin N. 2013. ‘Next generation’ biogeography: towards understanding the drivers of species diversification and persistence. Journal of Biogeography 40: 1013-1022.

Luquez V, Hall D, Albrectsen BR, Karlsson J, Ingvarsson P, Jansson S. 2008. Natural phenological variation in aspen (Populus tremula): the SwAsp collection. Tree Genetics and Genomes 4: 279-292.

Ma XF, Hall D, St. Onge KR, Jansson S, Ingvarsson PK. 2010. Genetic differentiation, clinal variation and phenotypic associations with growth cessation across the Populus tremula photoperiodic pathway. Genetics 186: 1033-1044.

McKown AD, Guy RD, Azam MS, Drewes EC, Quamme L. 2013. Seasonality and phenology alter functional leaf traits. Oecologia 172: 653-665.

Mousseau TA, Roff DA. 1987. Natural selection and the heritability of fitness components. Heredity 59: 181-197.

Neale DB, Ingvarsson PK. 2008. Population, quantitative and comparative genomics of adaptation in forest trees. Current Opinion in Plant Biology 11: 149-155.

Novembre J, Johnson T, Bryc K, Kutalik Z, Boyko AR, Auton A, Indap A, King KS, Bergmann S, Nelson MR et al. 2008. Genes mirror geography within Europe. Nature 456: 98-101.

Olson MS, Levsen N, Soolanayakanahally RY, Guy RD, Schroeder WR, Keller SR, Tiffin P. 2012. The adaptive potential of Populus balsamifera L. to phenology requirements in a warmer global climate. Molecular Ecology 22: 1214-1230.

Patterson N, Price AL, Reich D. 2006. Population structure and eigenanalysis. Plos Genetics 2: 2074-2093.

Pliura A, Zhang SY, MacKay J, Bousquet J. 2007. Genotypic variation in wood density and growth traits of poplar hybrids at four clonal trials. Forest Ecology and Management 238: 92-106.

R Core Development Team. 2011. R: a language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing.

Rae AM, Robinson KM, Street NR, Taylor G. 2004. Morphological and physiological traits influencing biomass productivity in short-rotation coppice poplar. Canadian Journal of Forest Research 34: 1488-1498.

Riemenschneider DE, Stelzer HE, Foster GS. 1996. Quantitative genetics of poplars and poplar hybrids. In: Stettler RF, Bradshaw HD Jr, Heilman PE, Hinckley TM, eds. Biology of Populus and its implications for management and conservation. Ottawa, ON, Canada: NRC Research Press, 159-181.

Rohde A, Bastien C, Boerjan W. 2011. Temperature signals contribute to the timing of photoperiodic growth cessation and bud set in poplar. Tree Physiology 31: 472-482.

Rohde A, Storme V, Jorge V, Gaudet M, Vitacolonna N, Fabbrini F, Ruttink T, Zaina G, Marron N, Dillen S et al. 2010. Bud set in poplar - genetic dissection of a complex trait in natural and hybrid populations. New Phytologist 189: 106-121.

Ruttink T, Arend M, Morreel K, Storme V, Rombauts S, Fromm J, Bhalerao RP, Boerjan W, Rohde A. 2007. A molecular timetable for apical bud formation and dormancy induction in poplar. Plant Cell 19: 2370-2390.

Savolainen O, Pyhäjärvi T, Knürr T. 2007. Gene flow and local adaptation in trees. Annual Review of Ecology Evolution and Systematics 38: 595-619.

Slavov GT, DiFazio SP, Martin J, Schackwitz W, Muchero W, Rodgers-Melnick E, Lipphardt MF, Pennacchio CP, Hellsten U, Pennacchio LA et al. 2012. Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa. New Phytologist 196: 713-725.

Slavov GT, Leonardi S, Adams WT, Strauss SH, DiFazio SP. 2010. Population substructure in continuous and fragmented stands of Populus trichocarpa. Heredity 105: 348-357.

Soolanayakanahally RY, Guy RD, Silim SN, Drewes EC, Schroeder WR. 2009. Enhanced assimilation rate and water use efficiency with latitude through increased photosynthetic capacity and internal conductance in balsam poplar (Populus balsamifera L.). Plant, Cell & Environment 32: 1821-1832.

Soolanayakanahally RY, Guy RD, Silim SN, Song M. 2013. Timing of photoperiodic competency causes phenological mismatch in balsam poplar (Populus balsamifera L.). Plant, Cell & Environment 36: 116-127.

Stapley J, Reger J, Feulner PG, Smadja C, Galindo J, Ekblom R, Bennison C, Ball AD, Beckerman AP, Slate J. 2010. Adaptation genomics: the next generation. Trends in Ecology & Evolution 25: 705-712.

Tuskan GA, DiFazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A et al. 2006. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313: 1596-1604.

Wang C, Zollner S, Rosenberg NA. 2012b. A quantitative comparison of the similarity between genes and geography in worldwide human populations. PLoS Genetics 8: e1002886.

Wang D, Sun Y, Stang P, Berlin JA, Wilcox MA, Li Q. 2009. Comparison of methods for correcting population stratification in a genome-wide association study of rheumatoid arthritis: principal component analysis versus multidimensional scaling. BMC Proceedings 3(Suppl 7): S109.

Wang T, Hamann A, Spittlehouse D, Murdock TN. 2012a. ClimateWNA - high-resolution spatial climate data for western North America. Journal of Applied Meteorology and Climatology 61: 16-29.

Xie C-Y, Ying CC, Yanchuk AD, Holowachuk DL. 2009. Ecotypic mode of regional differentiation caused by restricted gene migration: a case in black cottonwood (Populus trichocarpa) along the Pacific Northwest coast. Canadian Journal of Forest Research 39: 519-526.

Yanchuk AD, Dancik BP, Micko MM. 1984. Variation and heritability of wood density and fibre length of trembling aspen in Alberta, Canada. Silvae Genetica 33: 11-16.

Nejnovějších 20 citací...

Zobrazit více v
Medvik | PubMed

Sexual homomorphism in dioecious trees: extensive tests fail to detect sexual dimorphism in Populus †

. 2017 May 12 ; 7 (1) : 1831. [epub] 20170512

Evolutionary Quantitative Genomics of Populus trichocarpa

. 2015 ; 10 (11) : e0142864. [epub] 20151123

Najít záznam

Citační ukazatele

Nahrávání dat ...

Možnosti archivace

Nahrávání dat ...