Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations.
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G. Tuskan | P. Ranjan | S. DiFazio | L. Gunter | A. Brunner | Jin‐Gui Chen | W. Schackwitz | Joel A. Martin | G. Slavov | Eli Rodgers-Melnick | W. Muchero | L. Evans
[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..