Signatures of adaptation in the weedy rice genome

Evolutionary and social consequences of introgression of nontransgenic herbicide resistance from rice to weedy rice in Brazil

(2016) Aldo Merotto et al.   Evolutionary Applications

Fitness correlates of crop transgene flow into weedy populations: a case study of weedy rice in China and other examples

(2016) Bao-Rong Lu et al.   Evolutionary Applications

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

The Impact of Herbicide-Resistant Rice Technology on Phenotypic Diversity and Population Structure of United States Weedy Rice

(2014) N. R. Burgos et al.   PLANT PHYSIOLOGY

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

Current perspectives and the future of domestication studies

(2014) G. Larson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The 3,000 rice genomes project

(2014)   GigaScience

A Bountiful Harvest: Genomic Insights into Crop Domestication Phenotypes

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

Strategies to manage weedy rice in Asia

(2013) Bhagirath Singh Chauhan   CROP PROTECTION

The role ofBh4in parallel evolution of hull colour in domesticated and weedy rice

(2013) C. C. Vigueira et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

SweeD: Likelihood-Based Detection of Selective Sweeps in Thousands of Genomes

(2013) Pavlos Pavlidis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution of crop species: genetics of domestication and diversification

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

Microsatellite markers reveal multiple origins for Italian weedy rice

(2013) Annabelle Grimm et al.   Ecology and Evolution

Crop plants as models for understanding plant adaptation and diversification

(2013) Kenneth M. Olsen et al.   Frontiers in Plant Science

Population structure of the primary gene pool of Oryza sativa in Thailand

(2012) Tonapha Pusadee et al.   GENETIC RESOURCES AND CROP EVOLUTION

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

(2012) C C Vigueira et al.   HEREDITY

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Similar traits, different genes? Examining convergent evolution in related weedy rice populations

(2012) Carrie S. Thurber et al.   MOLECULAR ECOLOGY

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

(2012) Xuehui Huang et al.   NATURE

Weed Suppression Potential of ‘Rondo’ and Other Indica Rice Germplasm Lines

(2012) David R. Gealy et al.   WEED TECHNOLOGY

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Association Between Seed Dormancy and Pericarp Color Is Controlled by a Pleiotropic Gene That Regulates Abscisic Acid and Flavonoid Synthesis in Weedy Red Rice

(2011) Xing-You Gu et al.   GENETICS

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

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

(2011) Xun Xu et al.   NATURE BIOTECHNOLOGY

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Darwinian and demographic forces affecting human protein coding genes

(2009) R. Nielsen et al.   GENOME RESEARCH

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

Maximum Outcrossing Rate and Genetic Compatibility between Red Rice (Oryza sativa) Biotypes and Clearfield™ Rice

(2008) Vinod K. Shivrain et al.   WEED SCIENCE