Identifying genetic variants underlying phenotypic variation in plants without complete genomes

[1]  Matteo Comin,et al.  Benchmarking of alignment-free sequence comparison methods , 2019, Genome Biology.

[2]  P. Eastmond,et al.  Basic LEUCINE ZIPPER TRANSCRIPTION FACTOR67 Transactivates DELAY OF GERMINATION1 to Establish Primary Seed Dormancy in Arabidopsis. , 2019, The Plant cell.

[3]  A. Castro,et al.  Diploid Genome Assembly of the Wine Grape Carménère , 2019, G3: Genes, Genomes, Genetics.

[4]  Jonathan D. G. Jones,et al.  Resistance gene cloning from a wild crop relative by sequence capture and association genetics , 2019, Nature Biotechnology.

[5]  Christine G. Elsik,et al.  MaizeGDB 2018: the maize multi-genome genetics and genomics database , 2018, Nucleic Acids Res..

[6]  Daniel J. Kliebenstein,et al.  Digital Imaging Combined with Genome-Wide Association Mapping Links Loci to Plant-Pathogen Interaction Traits1[OPEN] , 2018, Plant Physiology.

[7]  Daniel L. Vera,et al.  The maize W22 genome provides a foundation for functional genomics and transposon biology , 2018, Nature Genetics.

[8]  P. Schnable,et al.  Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes , 2018, Nature Genetics.

[9]  Lior Pachter,et al.  Association mapping from sequencing reads using k-mers , 2017, bioRxiv.

[10]  Jie Luo,et al.  Rewiring of the Fruit Metabolome in Tomato Breeding , 2018, Cell.

[11]  Karsten M. Borgwardt,et al.  The AraGWAS Catalog: a curated and standardized Arabidopsis thaliana GWAS catalog , 2017, Nucleic Acids Res..

[12]  Heng Li,et al.  Minimap2: pairwise alignment for nucleotide sequences , 2017, Bioinform..

[13]  Jin-Wu Nam,et al.  The present and future of de novo whole-genome assembly , 2016, Briefings Bioinform..

[14]  Wendy S. Schackwitz,et al.  Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure , 2017, Nature Communications.

[15]  W. Busch,et al.  Natural Genetic Variation Shapes Root System Responses to Phytohormones in Arabidopsis , 2017, bioRxiv.

[16]  Jordan M. Eizenga,et al.  Genome graphs and the evolution of genome inference , 2017, bioRxiv.

[17]  David Goldblatt,et al.  Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration , 2017, bioRxiv.

[18]  Sanwen Huang,et al.  A chemical genetic roadmap to improved tomato flavor , 2017, Science.

[19]  Sebastian Deorowicz,et al.  KMC 3: counting and manipulating k‐mer statistics , 2017, Bioinform..

[20]  Karsten M. Borgwardt,et al.  AraPheno: a public database for Arabidopsis thaliana phenotypes , 2016, Nucleic Acids Res..

[21]  Karsten M. Borgwardt,et al.  1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana , 2016, Cell.

[22]  Eva-Maria Willing,et al.  Chromosome-level assembly of Arabidopsis thaliana Ler reveals the extent of translocation and inversion polymorphisms , 2016, Proceedings of the National Academy of Sciences.

[23]  J. Bergelson,et al.  Differentiation between MAMP Triggered Defenses in Arabidopsis thaliana , 2016, PLoS genetics.

[24]  F. Thibaud-Nissen,et al.  Araport11: a complete reannotation of the Arabidopsis thaliana reference genome , 2016, bioRxiv.

[25]  Jukka Corander,et al.  Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes , 2016, Nature Communications.

[26]  David A. Clifton,et al.  Identifying lineage effects when controlling for population structure improves power in bacterial association studies , 2015, Nature Microbiology.

[27]  Yingrui Li,et al.  Construction of the third-generation Zea mays haplotype map , 2015, bioRxiv.

[28]  K. Yahara,et al.  Enhanced biofilm formation and multi‐host transmission evolve from divergent genetic backgrounds in C ampylobacter jejuni , 2015, Environmental microbiology.

[29]  O. Kohany,et al.  Repbase Update, a database of repetitive elements in eukaryotic genomes , 2015, Mobile DNA.

[30]  Mark Abney,et al.  Permutation Testing in the Presence of Polygenic Variation , 2015, bioRxiv.

[31]  B. Berger,et al.  Efficient Bayesian mixed model analysis increases association power in large cohorts , 2014, Nature Genetics.

[32]  Kui Lin,et al.  Genomic analyses provide insights into the history of tomato breeding , 2014, Nature Genetics.

[33]  H. Mo,et al.  Exploiting Natural Variation of Secondary Metabolism Identifies a Gene Controlling the Glycosylation Diversity of Dihydroxybenzoic Acids in Arabidopsis thaliana , 2014, Genetics.

[34]  Rajeev K. Varshney,et al.  Structural variations in plant genomes , 2014, Briefings in functional genomics.

[35]  C. R. Linder,et al.  Association Mapping of Germination Traits in Arabidopsis thaliana Under Light and Nutrient Treatments: Searching for G×E Effects , 2014, G3: Genes, Genomes, Genetics.

[36]  Steven L Salzberg,et al.  DIAMUND: Direct Comparison of Genomes to Detect Mutations , 2013, Human mutation.

[37]  Jason A. Corwin,et al.  Cytoplasmic genetic variation and extensive cytonuclear interactions influence natural variation in the metabolome , 2013, eLife.

[38]  Mariska A Nijenhuis-de Vries,et al.  NON-SMOKY GLYCOSYLTRANSFERASE1 Prevents the Release of Smoky Aroma from Tomato Fruit[W][OPEN] , 2013, Plant Cell.

[39]  Keith A. Jolley,et al.  Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter , 2013, Proceedings of the National Academy of Sciences.

[40]  Tatiana I Axenovich,et al.  Rapid variance components–based method for whole-genome association analysis , 2012, Nature Genetics.

[41]  M. Stephens,et al.  Genome-wide Efficient Mixed Model Analysis for Association Studies , 2012, Nature Genetics.

[42]  Sergey I. Nikolenko,et al.  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..

[43]  Daniel W. A. Buchan,et al.  The tomato genome sequence provides insights into fleshy fruit evolution , 2012, Nature.

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

[45]  G. McVean,et al.  De novo assembly and genotyping of variants using colored de Bruijn graphs , 2011, Nature Genetics.

[46]  Gonçalo R. Abecasis,et al.  The variant call format and VCFtools , 2011, Bioinform..

[47]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer , 2011, Nature Biotechnology.

[48]  D. Kliebenstein,et al.  The Complex Genetic Architecture of the Metabolome , 2010, PLoS genetics.

[49]  Muhammad Ali Amer,et al.  Genome-wide association study of 107 phenotypes in a common set of Arabidopsis thaliana inbred lines , 2010, Nature.

[50]  Robert J. Elshire,et al.  A First-Generation Haplotype Map of Maize , 2009, Science.

[51]  Dawn H. Nagel,et al.  The B73 Maize Genome: Complexity, Diversity, and Dynamics , 2009, Science.

[52]  N. Warthmann,et al.  Simultaneous alignment of short reads against multiple genomes , 2009, Genome Biology.

[53]  D. Heckerman,et al.  Efficient Control of Population Structure in Model Organism Association Mapping , 2008, Genetics.

[54]  Manuel A. R. Ferreira,et al.  PLINK: a tool set for whole-genome association and population-based linkage analyses. , 2007, American journal of human genetics.

[55]  Wei Zhao,et al.  Panzea: a database and resource for molecular and functional diversity in the maize genome , 2005, Nucleic Acids Res..

[56]  N. Risch,et al.  A comparison of linkage disequilibrium measures for fine-scale mapping. , 1995, Genomics.