Genomic variation associated with local adaptation of weedy rice during de-domestication

Population genomics identifies the origin and signatures of selection of Korean weedy rice

(2016) Qiang He et al.   PLANT BIOTECHNOLOGY JOURNAL

Feralisation targets different genomic loci to domestication in the chicken

(2016) M. Johnsson et al.   Nature Communications

Rice Domestication Revealed by Reduced Shattering of Archaeological rice from the Lower Yangtze valley

(2016) Yunfei Zheng et al.   Scientific Reports

More than one way to evolve a weed: parallel evolution of US weedy rice through independent genetic mechanisms

(2015) Xinshuai Qi et al.   MOLECULAR ECOLOGY

Detecting balancing selection in genomes: limits and prospects

(2015) Anna Fijarczyk et al.   MOLECULAR ECOLOGY

Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection

(2015) Weibo Xie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cytoplasmic-genetic male sterility gene provides direct evidence for some hybrid rice recently evolving into weedy rice

(2015) Jingxu Zhang et al.   Scientific Reports

The evolution of flowering strategies in US weedy rice

(2014) Carrie S. Thurber et al.   AMERICAN JOURNAL OF BOTANY

Repression of Expression Leads to Root System Growth Suppression in Rice

(2014) Shichun Qiu et al.   CROP SCIENCE

PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R

(2014) Bastian Pfeifer et al.   MOLECULAR BIOLOGY AND EVOLUTION

Malaysian weedy rice shows its true stripes: wildOryzaand elite rice cultivars shape agricultural weed evolution in Southeast Asia

(2014) Beng-Kah Song et al.   MOLECULAR ECOLOGY

Genome re-sequencing suggested a weedy rice origin from domesticated indica-japonica hybridization: a case study from southern China

(2014) Jie Qiu et al.   PLANTA

Allele Distributions at Hybrid Incompatibility Loci Facilitate the Potential for Gene Flow between Cultivated and Weedy Rice in the US

(2014) Stephanie M. Craig et al.   PLoS One

Fine mapping and candidate gene analysis of the novel thermo-sensitive genic male sterility tms9-1 gene in rice

(2014) Yongbin Qi et al.   THEORETICAL AND APPLIED GENETICS

A Bountiful Harvest: Genomic Insights into Crop Domestication Phenotypes

(2013) Kenneth M. Olsen et al.   Annual Review of Plant Biology

The genomic signature of dog domestication reveals adaptation to a starch-rich diet

(2013) Erik Axelsson et al.   NATURE

Evolution of crop species: genetics of domestication and diversification

(2013) Rachel S. Meyer et al.   NATURE REVIEWS GENETICS

GenGIS 2: Geospatial Analysis of Traditional and Genetic Biodiversity, with New Gradient Algorithms and an Extensible Plugin Framework

(2013) Donovan H. Parks et al.   PLoS One

Ehd4 Encodes a Novel and Oryza-Genus-Specific Regulator of Photoperiodic Flowering in Rice

(2013) He Gao et al.   PLoS Genetics

A high-performance computing toolset for relatedness and principal component analysis of SNP data

(2012) X. Zheng et al.   BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

The red queen in the corn: agricultural weeds as models of rapid adaptive evolution

(2012) C C Vigueira et al.   HEREDITY

A map of rice genome variation reveals the origin of cultivated rice

(2012) Xuehui Huang et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Introgression and selection shaping the genome and adaptive loci of weedy rice in northern China

(2012) Jian Sun et al.   NEW PHYTOLOGIST

Constitutive expression of rice WRKY30 gene increases the endogenous jasmonic acid accumulation, PR gene expression and resistance to fungal pathogens in rice

(2012) Xixu Peng et al.   PLANTA

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

The long and the short of it: SD1 polymorphism and the evolution of growth trait divergence in U.S. weedy rice

(2011) MICHAEL REAGON et al.   MOLECULAR ECOLOGY

Molecular evidence for a single evolutionary origin of domesticated rice

(2011) J. Molina et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic patterns of nucleotide diversity in divergent populations of U.S. weedy rice

(2010) Michael Reagon et al.   BMC EVOLUTIONARY BIOLOGY

Crops gone wild: evolution of weeds and invasives from domesticated ancestors

(2010) Norman C. Ellstrand et al.   Evolutionary Applications

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

agriGO: a GO analysis toolkit for the agricultural community

(2010) Zhou Du et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

DnaSP v5: a software for comprehensive analysis of DNA polymorphism data

(2009) P. Librado et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Selection on grain shattering genes and rates of rice domestication

(2009) Lin-Bin Zhang et al.   NEW PHYTOLOGIST

Inactivation of the CTD phosphatase-like geneOsCPL1enhances the development of the abscission layer and seed shattering in rice

(2009) Hyeonso Ji et al.   PLANT JOURNAL

The Domestication Process and Domestication Rate in Rice: Spikelet Bases from the Lower Yangtze

(2009) D. Q Fuller et al.   SCIENCE

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

(2009) Ryan N. Gutenkunst et al.   PLoS Genetics

Overexpression of a TFIIIA-type zinc finger protein geneZFP252enhances drought and salt tolerance in rice (Oryza sativaL.)

(2008) Dong-Qing Xu et al.   FEBS LETTERS

Adaptation from standing genetic variation

(2007) R BARRETT et al.   TRENDS IN ECOLOGY & EVOLUTION