Tracing the ancestry of modern bread wheats

[1]  Hadi Quesneville,et al.  Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data , 2018, Genome Biology.

[2]  Paul H. C. Eilers,et al.  Correcting for spatial heterogeneity in plant breeding experiments with P-splines , 2018 .

[3]  H. Daetwyler,et al.  Genetic Diversity, Population Structure and Ancestral Origin of Australian Wheat , 2017, Front. Plant Sci..

[4]  John G Kenny,et al.  Hidden variation in polyploid wheat drives local adaptation , 2017, bioRxiv.

[5]  Dawei Huang,et al.  Candidate loci involved in domestication and improvement detected by a published 90K wheat SNP array , 2017, Scientific Reports.

[6]  A. Nadolska-Orczyk,et al.  Major genes determining yield-related traits in wheat and barley , 2017, Theoretical and Applied Genetics.

[7]  H. Quesneville,et al.  Reconciling the evolutionary origin of bread wheat (Triticum aestivum). , 2017, The New phytologist.

[8]  Joost J. B. Keurentjes,et al.  Genetic architecture of plant stress resistance: multi‐trait genome‐wide association mapping , 2016, The New phytologist.

[9]  M. Blum,et al.  Pcadapt: An R Package to Perform Genome Scans for Selection Based on Principal Component Analysis , 2016, bioRxiv.

[10]  Alain Charcosset,et al.  Genome-Wide Analysis of Yield in Europe: Allelic Effects Vary with Drought and Heat Scenarios1[OPEN] , 2016, Plant Physiology.

[11]  Gary D. Bader,et al.  AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations , 2016, F1000Research.

[12]  Tal Galili,et al.  dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering , 2015, Bioinform..

[13]  D. Hume,et al.  Exome Sequencing: Current and Future Perspectives , 2015, G3: Genes, Genomes, Genetics.

[14]  B. Kromer,et al.  Tracing the genetic origin of Europe's first farmers reveals insights into their social organization , 2015, Proceedings of the Royal Society B: Biological Sciences.

[15]  Neil Hall,et al.  A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes , 2015, Genome Biology.

[16]  R. Nielsen,et al.  ANGSD: Analysis of Next Generation Sequencing Data , 2014, BMC Bioinformatics.

[17]  A. von Haeseler,et al.  IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies , 2014, Molecular biology and evolution.

[18]  Roland Eils,et al.  circlize implements and enhances circular visualization in R , 2014, Bioinform..

[19]  Simon H. Martin,et al.  Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci , 2014, bioRxiv.

[20]  N. H. Nielsen,et al.  Genetic Diversity and Population Structure Analysis of European Hexaploid Bread Wheat (Triticum aestivum L.) Varieties , 2014, PloS one.

[21]  L. Excoffier,et al.  Ignoring heterozygous sites biases phylogenomic estimates of divergence times: implications for the evolutionary history of microtus voles. , 2014, Molecular biology and evolution.

[22]  E. Kuhn,et al.  Recovering Power in Association Mapping Panels with Variable Levels of Linkage Disequilibrium , 2014, Genetics.

[23]  T. A. Brown,et al.  Reticulated Origin of Domesticated Emmer Wheat Supports a Dynamic Model for the Emergence of Agriculture in the Fertile Crescent , 2013, PloS one.

[24]  J. Dvorak,et al.  Aegilops tauschii single nucleotide polymorphisms shed light on the origins of wheat D-genome genetic diversity and pinpoint the geographic origin of hexaploid wheat. , 2013, The New phytologist.

[25]  J. Anderson,et al.  Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars , 2013, Proceedings of the National Academy of Sciences.

[26]  Minh Anh Nguyen,et al.  Ultrafast Approximation for Phylogenetic Bootstrap , 2013, Molecular biology and evolution.

[27]  M. Feldman,et al.  Genome Evolution Due to Allopolyploidization in Wheat , 2012, Genetics.

[28]  Chris-Carolin Schön,et al.  synbreed: a framework for the analysis of genomic prediction data using R , 2012, Bioinform..

[29]  Liam J. Revell,et al.  phytools: an R package for phylogenetic comparative biology (and other things) , 2012 .

[30]  David Reich,et al.  Testing for ancient admixture between closely related populations. , 2011, Molecular biology and evolution.

[31]  Y. Matsuoka.  Evolution of polyploid triticum wheats under cultivation: the role of domestication, natural hybridization and allopolyploid speciation in their diversification. , 2011, Plant & cell physiology.

[32]  Hannes Feilhauer,et al.  A brute-force approach to vegetation classification , 2010 .

[33]  Robert Tibshirani,et al.  A Framework for Feature Selection in Clustering , 2010, Journal of the American Statistical Association.

[34]  William J. Astle,et al.  Population Structure and Cryptic Relatedness in Genetic Association Studies , 2009, 1010.4681.

[35]  J. Bocquet-Appel,et al.  Detection of diffusion and contact zones of early farming in Europe from the space-time distribution of 14C dates , 2009 .

[36]  Terence A Brown,et al.  The complex origins of domesticated crops in the Fertile Crescent. , 2009, Trends in ecology & evolution.

[37]  Sébastien Lê,et al.  FactoMineR: An R Package for Multivariate Analysis , 2008 .

[38]  F. V. van Eeuwijk,et al.  A Mixed-Model Quantitative Trait Loci (QTL) Analysis for Multiple-Environment Trial Data Using Environmental Covariables for QTL-by-Environment Interactions, With an Example in Maize , 2007, Genetics.

[39]  J. Dvorak,et al.  The structure of wild and domesticated emmer wheat populations, gene flow between them, and the site of emmer domestication , 2007, Theoretical and Applied Genetics.

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

[41]  K. Tanno,et al.  How Fast Was Wild Wheat Domesticated? , 2006, Science.

[42]  J. Li,et al.  Adjusting multiple testing in multilocus analyses using the eigenvalues of a correlation matrix , 2005, Heredity.

[43]  Robert Tibshirani,et al.  Hybrid hierarchical clustering with applications to microarray data. , 2005, Biostatistics.

[44]  Steven G. Schroeder,et al.  The Effects of Artificial Selection on the Maize Genome , 2005, Science.

[45]  S. Nasuda,et al.  Durum wheat as a candidate for the unknown female progenitor of bread wheat: an empirical study with a highly fertile F1 hybrid with Aegilops tauschii Coss. , 2004, Theoretical and Applied Genetics.

[46]  G. Kovács,et al.  ORIGIN AND TAXONOMY OF WHEAT IN THE LIGHT OF RECENT RESEARCH , 2000 .

[47]  K. Roeder,et al.  Genomic Control for Association Studies , 1999, Biometrics.

[48]  J. Dvorak,et al.  Structural evolution of wheat chromosomes 4A, 5A, and 7B and its impact on recombination , 1995, Theoretical and Applied Genetics.

[49]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[50]  A. Korol,et al.  Dissection of powdery mildew resistance uncover different resistance types in the Triticum turgidum L. gene pool , 2008 .

[51]  Sue J. Welham,et al.  Likelihood Ratio Tests for Fixed Model Terms using Residual Maximum Likelihood , 1997 .