Identifying genetic variants underlying phenotypic variation in plants without complete genomes

Diploid Genome Assembly of the Wine Grape Carménère

(2019) Andrea Minio et al.   G3-Genes Genomes Genetics

Resistance gene cloning from a wild crop relative by sequence capture and association genetics

(2019) Sanu Arora et al.   NATURE BIOTECHNOLOGY

Basic LEUCINE ZIPPER TRANSCRIPTION FACTOR 67 transactivates DELAY OF GERMINATION 1 to establish primary seed dormancy in Arabidopsis

(2019) Fiona M. Bryant et al.   PLANT CELL

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Rewiring of the Fruit Metabolome in Tomato Breeding

(2018) Guangtao Zhu et al.   CELL

Natural Genetic Variation Shapes Root System Responses to Phytohormones in Arabidopsis

(2018) Daniela Ristova et al.   PLANT JOURNAL

Association mapping from sequencing reads using k-mers

(2018) Atif Rahman et al.   eLife

The maize W22 genome provides a foundation for functional genomics and transposon biology

(2018) Nathan M. Springer et al.   NATURE GENETICS

Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes

(2018) Silong Sun et al.   NATURE GENETICS

Digital Imaging Combined with Genome-Wide Association Mapping Links Loci to Plant-Pathogen Interaction Traits

(2018) Rachel F Fordyce et al.   PLANT PHYSIOLOGY

MaizeGDB 2018: the maize multi-genome genetics and genomics database

(2018) John L Portwood et al.   NUCLEIC ACIDS RESEARCH

Genome graphs and the evolution of genome inference

(2017) Benedict Paten et al.   GENOME RESEARCH

The AraGWAS Catalog: a curated and standardized Arabidopsis thaliana GWAS catalog

(2017) Matteo Togninalli et al.   NUCLEIC ACIDS RESEARCH

Araport11: a complete reannotation of theArabidopsis thalianareference genome

(2017) Chia-Yi Cheng et al.   PLANT JOURNAL

A chemical genetic roadmap to improved tomato flavor

(2017) Denise Tieman et al.   SCIENCE

Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure

(2017) Sean P. Gordon et al.   Nature Communications

Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration

(2017) John A Lees et al.   eLife

Construction of the third-generation Zea mays haplotype map

(2017) Robert Bukowski et al.   GigaScience

1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

(2016) Carlos Alonso-Blanco et al.   CELL

AraPheno: a public database for Arabidopsis thaliana phenotypes

(2016) Ümit Seren et al.   NUCLEIC ACIDS RESEARCH

Chromosome-level assembly ofArabidopsis thalianaLerreveals the extent of translocation and inversion polymorphisms

(2016) Luis Zapata et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differentiation between MAMP Triggered Defenses in Arabidopsis thaliana

(2016) Madlen Vetter et al.   PLoS Genetics

Enhanced biofilm formation and multi-host transmission evolve from divergent genetic backgrounds inCampylobacter jejuni

(2015) Ben Pascoe et al.   ENVIRONMENTAL MICROBIOLOGY

Permutation Testing in the Presence of Polygenic Variation

(2015) Mark Abney   GENETIC EPIDEMIOLOGY

Efficient Bayesian mixed-model analysis increases association power in large cohorts

(2015) Po-Ru Loh et al.   NATURE GENETICS

Structural variations in plant genomes

(2014) R. K. Saxena et al.   Briefings in Functional Genomics

Exploiting Natural Variation of Secondary Metabolism Identifies a Gene Controlling the Glycosylation Diversity of Dihydroxybenzoic Acids in Arabidopsis thaliana

(2014) X. Li et al.   GENETICS

Genomic analyses provide insights into the history of tomato breeding

(2014) Tao Lin et al.   NATURE GENETICS

Association Mapping of Germination Traits in Arabidopsis thaliana Under Light and Nutrient Treatments: Searching for G×E Effects

(2014) Ginnie D. Morrison et al.   G3-Genes Genomes Genetics

DIAMUND: Direct Comparison of Genomes to Detect Mutations

(2013) Steven L. Salzberg et al.   HUMAN MUTATION

NON-SMOKY GLYCOSYLTRANSFERASE1 Prevents the Release of Smoky Aroma from Tomato Fruit

(2013) Y. M. Tikunov et al.   PLANT CELL

Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter

(2013) S. K. Sheppard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

De novo assembly and genotyping of variants using colored de Bruijn graphs

(2012) Zamin Iqbal et al.   NATURE GENETICS

Rapid variance components–based method for whole-genome association analysis

(2012) Gulnara R Svishcheva et al.   NATURE GENETICS

Genome-wide efficient mixed-model analysis for association studies

(2012) Xiang Zhou et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines

(2010) Susanna Atwell et al.   NATURE

The Complex Genetic Architecture of the Metabolome

(2010) Eva K. F. Chan et al.   PLoS Genetics

A First-Generation Haplotype Map of Maize

(2009) M. A. Gore et al.   SCIENCE

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

Simultaneous alignment of short reads against multiple genomes

(2009) Korbinian Schneeberger et al.   GENOME BIOLOGY

Efficient Control of Population Structure in Model Organism Association Mapping

(2008) H. M. Kang et al.   GENETICS