Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations.

[1]  Q. Cronk,et al.  Geographical and environmental gradients shape phenotypic trait variation and genetic structure in Populus trichocarpa. , 2014, The New phytologist.

[2]  M. Stephens,et al.  Efficient Algorithms for Multivariate Linear Mixed Models in Genome-wide Association Studies , 2013, Nature Methods.

[3]  G. Tuskan,et al.  Genome-wide association mapping for wood characteristics in Populus identifies an array of candidate single nucleotide polymorphisms. , 2013, The New phytologist.

[4]  Mark Culp,et al.  Predicting whole genome protein interaction networks from primary sequence data in model and non-model organisms using ENTS , 2013, BMC Genomics.

[5]  N. Medina-Escobar,et al.  The Ureide-Degrading Reactions of Purine Ring Catabolism Employ Three Amidohydrolases and One Aminohydrolase in Arabidopsis, Soybean, and Rice1[W] , 2013, Plant Physiology.

[6]  Wei Li,et al.  A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica) , 2013, Nature Genetics.

[7]  M. Morgante,et al.  Breeding with rare defective alleles (BRDA): a natural Populus nigra HCT mutant with modified lignin as a case study. , 2013, The New phytologist.

[8]  Hongwei Zhao,et al.  Genome-wide identification of the class III aminotransferase gene family in rice and expression analysis under abiotic stress , 2013, Genes & Genomics.

[9]  Katja E. Jaeger,et al.  Interlocking Feedback Loops Govern the Dynamic Behavior of the Floral Transition in Arabidopsis[W][OA] , 2013, Plant Cell.

[10]  Wendy S. Schackwitz,et al.  A 34K SNP genotyping array for Populus trichocarpa: Design, application to the study of natural populations and transferability to other Populus species , 2013, Molecular ecology resources.

[11]  Eric S. Lander,et al.  Identifying Recent Adaptations in Large-Scale Genomic Data , 2013, Cell.

[12]  K. Lindblad-Toh,et al.  The genomic signature of dog domestication reveals adaptation to a starch-rich diet , 2013, Nature.

[13]  O. Delaneau,et al.  Supplementary Information for ‘ Improved whole chromosome phasing for disease and population genetic studies ’ , 2012 .

[14]  Huanming Yang,et al.  Whole-genome sequencing of giant pandas provides insights into demographic history and local adaptation , 2012, Nature Genetics.

[15]  Wendy S. Schackwitz,et al.  Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa. , 2012, The New phytologist.

[16]  Kenny Q. Ye,et al.  An integrated map of genetic variation from 1,092 human genomes , 2012, Nature.

[17]  G. Coop,et al.  Robust Identification of Local Adaptation from Allele Frequencies , 2012, Genetics.

[18]  M. Hufford,et al.  Complex Patterns of Local Adaptation in Teosinte , 2012, Genome biology and evolution.

[19]  W. Miller,et al.  Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change , 2012, Proceedings of the National Academy of Sciences.

[20]  Xun Xu,et al.  Comparative population genomics of maize domestication and improvement , 2012, Nature Genetics.

[21]  J. Chen,et al.  Genome-wide genetic changes during modern breeding of maize , 2012, Nature Genetics.

[22]  Eran Halperin,et al.  A model-based approach for analysis of spatial structure in genetic data , 2012, Nature Genetics.

[23]  Pablo Cingolani,et al.  © 2012 Landes Bioscience. Do not distribute. , 2022 .

[24]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[25]  A. Califano,et al.  PFT1, the MED25 subunit of the plant Mediator complex, promotes flowering through CONSTANS dependent and independent mechanisms in Arabidopsis. , 2012, The Plant journal : for cell and molecular biology.

[26]  Tongli Wang,et al.  ClimateWNA—High-Resolution Spatial Climate Data for Western North America , 2012 .

[27]  Ari Pekka Mähönen,et al.  Callose biosynthesis regulates symplastic trafficking during root development. , 2011, Developmental cell.

[28]  Qian Qian,et al.  Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm , 2011, Nature Genetics.

[29]  Heng Li,et al.  A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data , 2011, Bioinform..

[30]  M. Nordborg,et al.  A Map of Local Adaptation in Arabidopsis thaliana , 2011, Science.

[31]  Joy Bergelson,et al.  References and Notes Supporting Online Material Adaptation to Climate across the Arabidopsis Thaliana Genome , 2022 .

[32]  Karsten M. Borgwardt,et al.  Whole-genome sequencing of multiple Arabidopsis thaliana populations , 2011, Nature Genetics.

[33]  B. Browning,et al.  Haplotype phasing: existing methods and new developments , 2011, Nature Reviews Genetics.

[34]  G. Page,et al.  FLOWERING LOCUS T duplication coordinates reproductive and vegetative growth in perennial poplar , 2011, Proceedings of the National Academy of Sciences.

[35]  D. Grattapaglia,et al.  Genomic selection in forest tree breeding , 2011, Tree Genetics & Genomes.

[36]  D. Neale,et al.  Forest tree genomics: growing resources and applications , 2011, Nature Reviews Genetics.

[37]  P. Visscher,et al.  GCTA: a tool for genome-wide complex trait analysis. , 2011, American journal of human genetics.

[38]  J. Kangasjärvi,et al.  Chilling of Dormant Buds Hyperinduces FLOWERING LOCUS T and Recruits GA-Inducible 1,3-β-Glucanases to Reopen Signal Conduits and Release Dormancy in Populus[W][OA] , 2011, Plant Cell.

[39]  Liang Tang,et al.  PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database , 2010, Nucleic Acids Res..

[40]  M. Nordborg,et al.  Conditions Under Which Genome-Wide Association Studies Will be Positively Misleading , 2010, Genetics.

[41]  Meng Li,et al.  Genome-wide association studies of 14 agronomic traits in rice landraces , 2010, Nature Genetics.

[42]  Mark F. Davis,et al.  Association genetics of traits controlling lignin and cellulose biosynthesis in black cottonwood (Populus trichocarpa, Salicaceae) secondary xylem. , 2010, The New phytologist.

[43]  Jonathan K. Pritchard,et al.  Adaptation – not by sweeps alone , 2010, Nature Reviews Genetics.

[44]  Alkes L. Price,et al.  New approaches to population stratification in genome-wide association studies , 2010, Nature Reviews Genetics.

[45]  James A. Birchler,et al.  The gene balance hypothesis: implications for gene regulation, quantitative traits and evolution. , 2010, The New phytologist.

[46]  H. Kang,et al.  Variance component model to account for sample structure in genome-wide association studies , 2010, Nature Genetics.

[47]  S. Strauss,et al.  Populus CEN/TFL1 regulates first onset of flowering, axillary meristem identity and dormancy release in Populus. , 2010, The Plant journal : for cell and molecular biology.

[48]  Michael Freeling,et al.  Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition. , 2009, Annual review of plant biology.

[49]  B. Browning,et al.  A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. , 2009, American journal of human genetics.

[50]  Haibao Tang,et al.  Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. , 2008, Genome research.

[51]  G. Bonan Forests and Climate Change: Forcings, Feedbacks, and the Climate Benefits of Forests , 2008, Science.

[52]  S. DiFazio,et al.  Extending Genomics to Natural Communities and Ecosystems , 2008, Science.

[53]  F. Dudbridge,et al.  Estimation of significance thresholds for genomewide association scans , 2008, Genetic epidemiology.

[54]  T. Knürr,et al.  Gene Flow and Local Adaptation in Trees , 2007 .

[55]  Stefan Jansson,et al.  ADAPTIVE POPULATION DIFFERENTIATION IN PHENOLOGY ACROSS A LATITUDINAL GRADIENT IN EUROPEAN ASPEN (POPULUS TREMULA, L.): A COMPARISON OF NEUTRAL MARKERS, CANDIDATE GENES AND PHENOTYPIC TRAITS , 2007, Evolution; international journal of organic evolution.

[56]  Philip L. F. Johnson,et al.  Accounting for bias from sequencing error in population genetic estimates. , 2007, Molecular biology and evolution.

[57]  Stephane Rombauts,et al.  A Molecular Timetable for Apical Bud Formation and Dormancy Induction in Poplar[W] , 2007, The Plant Cell Online.

[58]  C. Douglas,et al.  Populus: a model system for plant biology. , 2007, Annual review of plant biology.

[59]  D. Reich,et al.  Population Structure and Eigenanalysis , 2006, PLoS genetics.

[60]  C. Parmesan Ecological and Evolutionary Responses to Recent Climate Change , 2006 .

[61]  M. Gribskov,et al.  The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray) , 2006, Science.

[62]  Stefan Jansson,et al.  CO/FT Regulatory Module Controls Timing of Flowering and Seasonal Growth Cessation in Trees , 2006, Science.

[63]  J. Pritchard,et al.  A Map of Recent Positive Selection in the Human Genome , 2006, PLoS biology.

[64]  P. Ingvarsson,et al.  Clinal Variation in phyB2, a Candidate Gene for Day-Length-Induced Growth Cessation and Bud Set, Across a Latitudinal Gradient in European Aspen (Populus tremula) , 2006, Genetics.

[65]  J. Goudet,et al.  The Effects of Dominance, Regular Inbreeding and Sampling Design on QST, an Estimator of Population Differentiation for Quantitative Traits , 2006, Genetics.

[66]  J. Webster,et al.  Loss of foundation species: consequences for the structure and dynamics of forested ecosystems , 2005 .

[67]  Jeroen Raes,et al.  Duplication and divergence: the evolution of new genes and old ideas. , 2004, Annual review of genetics.

[68]  K. Scholthof Tobacco mosaic virus: a model system for plant biology. , 2004, Annual review of phytopathology.

[69]  D. Neale,et al.  From genotype to phenotype: unraveling the complexities of cold adaptation in forest trees , 2003 .

[70]  Pardis C Sabeti,et al.  Detecting recent positive selection in the human genome from haplotype structure , 2002, Nature.

[71]  B. Charlesworth Measures of divergence between populations and the effect of forces that reduce variability. , 1998, Molecular biology and evolution.

[72]  K. Spitze Population structure in Daphnia obtusa: quantitative genetic and allozymic variation. , 1993, Genetics.

[73]  O. Langlet Two hundred years genecology. , 1971 .

[74]  S. Mane,et al.  Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus. , 2012, Genome research.

[75]  Zonglie Hong,et al.  CalS7 encodes a callose synthase responsible for callose deposition in the phloem. , 2011, The Plant journal : for cell and molecular biology.

[76]  Bjarni J. Vilhjálmsson,et al.  Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines , 2010 .

[77]  Tongli Wang,et al.  Integrating environmental and genetic effects to predict responses of tree populations to climate. , 2010, Ecological applications : a publication of the Ecological Society of America.

[78]  Claude-Alain H. Roten,et al.  Fast and accurate short read alignment with Burrows–Wheeler transform , 2009, Bioinform..

[79]  Holly M. Mortensen,et al.  Convergent adaptation of human lactase persistence in Africa and Europe , 2007, Nature Genetics.

[80]  A. Force,et al.  The probability of duplicate gene preservation by subfunctionalization. , 2000, Genetics.

[81]  T. Hinckley,et al.  Biology of populus and its implications for management and conservation , 1996 .

[82]  T. Perry,et al.  Ecotypic Variation of the Photoperiodic Response in Populus , 1954, Journal of the Arnold Arboretum..