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

Mapping of Seed Shattering Loci Provides Insights into Origin of Weedy Rice and Rice Domestication

(2013) Prasanta K. Subudhi et al.   JOURNAL OF HEREDITY

PlantGSEA: a gene set enrichment analysis toolkit for plant community

(2013) Xin Yi et al.   NUCLEIC ACIDS RESEARCH

A model of the relationship between weedy rice seed-bank dynamics and rice-crop infestation and damage in Jiangsu Province, China

(2013) Zheng Zhang et al.   PEST MANAGEMENT SCIENCE

Resequencing rice genomes: an emerging new era of rice genomics

(2013) Xuehui Huang et al.   TRENDS IN GENETICS

The Genomic Signature of Crop-Wild Introgression in Maize

(2013) Matthew B. Hufford 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

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

Genetic Control of Seed Shattering in Rice by the APETALA2 Transcription Factor SHATTERING ABORTION1

(2012) Y. Zhou et al.   PLANT CELL

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

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

The contribution of intersubspecific hybridization to the breeding of super-high-yielding japonica rice in northeast China

(2012) Jian Sun et al.   THEORETICAL AND APPLIED GENETICS

Sequence polymorphisms in wild, weedy, and cultivated rice suggest seed-shattering locus sh4 played a minor role in Asian rice domestication

(2012) Yongqing Zhu et al.   Ecology and Evolution

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

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

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

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

(2011) Xun Xu et al.   NATURE BIOTECHNOLOGY

Introgression from cultivated rice influences genetic differentiation of weedy rice populations at a local spatial scale

(2011) Zhuxi Jiang et al.   THEORETICAL AND APPLIED GENETICS

Dating the age of admixture via wavelet transform analysis of genome-wide data

(2011) Irina Pugach et al.   GENOME BIOLOGY

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

(2010) Michael Reagon et al.   BMC EVOLUTIONARY BIOLOGY

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

(2010) A. McKenna et al.   GENOME RESEARCH

Seeing red: the origin of grain pigmentation in US weedy rice

(2010) BRIANA L. GROSS et al.   MOLECULAR ECOLOGY

Molecular evolution of shattering loci in U.S. weedy rice

(2010) CARRIE S. THURBER et al.   MOLECULAR ECOLOGY

agriGO: a GO analysis toolkit for the agricultural community

(2010) Zhou Du et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Selection on grain shattering genes and rates of rice domestication

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

Genetic Diversity and Relationship of Weedy Rice in Taizhou City, Jiangsu Province, China

(2009) Juan ZHANG et al.   Rice Science

Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication

(2008) Y. Yu et al.   PLANT CELL

The evolving story of rice evolution

(2008) Duncan A. Vaughan et al.   PLANT SCIENCE