Whole-genome resequencing reveals Brassica napus origin and genetic loci involved in its improvement

A 2.833-kb Insertion in BnFLC.A2 and Its Homeologous Exchange with BnFLC.C2 during Breeding Selection Generated Early-Flowering Rapeseed

(2018) Lei Chen et al.   Molecular Plant

Genomic inferences of domestication events are corroborated by written records in Brassica rapa

(2017) Xinshuai Qi et al.   MOLECULAR ECOLOGY

Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication

(2017) Maojun Wang et al.   NATURE GENETICS

The high-quality genome of Brassica napus cultivar ‘ZS11’ reveals the introgression history in semi-winter morphotype

(2017) Fengming Sun et al.   PLANT JOURNAL

Genotype Imputation with Millions of Reference Samples

(2016) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A diamond in the ruff

(2016)   NATURE GENETICS

The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection

(2016) Jinghua Yang et al.   NATURE GENETICS

Robust and scalable inference of population history from hundreds of unphased whole genomes

(2016) Jonathan Terhorst et al.   NATURE GENETICS

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean

(2015) Zhengkui Zhou et al.   NATURE BIOTECHNOLOGY

FLOR-ID: an interactive database of flowering-time gene networks inArabidopsis thaliana

(2015) Frédéric Bouché et al.   NUCLEIC ACIDS RESEARCH

Natural variation inARF18gene simultaneously affects seed weight and silique length in polyploid rapeseed

(2015) Jing Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Wheat waxy proteins: polymorphism, molecular characterization and effects on starch properties

(2015) Carlos Guzmán et al.   THEORETICAL AND APPLIED GENETICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

selscan: An Efficient Multithreaded Program to Perform EHH-Based Scans for Positive Selection

(2014) Z. A. Szpiech et al.   MOLECULAR BIOLOGY AND EVOLUTION

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic analyses provide insights into the history of tomato breeding

(2014) Tao Lin et al.   NATURE GENETICS

Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

(2014) B. Chalhoub et al.   SCIENCE

Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea

(2014) Isobel AP Parkin et al.   GENOME BIOLOGY

BRANCHED1 Promotes Axillary Bud Dormancy in Response to Shade in Arabidopsis

(2013) E. Gonzalez-Grandio et al.   PLANT CELL

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

The transcription factor AtDOF4.2 regulates shoot branching and seed coat formation inArabidopsis

(2012) Hong-Feng Zou et al.   BIOCHEMICAL JOURNAL

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

NRT/PTR transporters are essential for translocation of glucosinolate defence compounds to seeds

(2012) Hussam Hassan Nour-Eldin et al.   NATURE

NPR3 and NPR4 are receptors for the immune signal salicylic acid in plants

(2012) Zheng Qing Fu et al.   NATURE

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

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

(2011) Xun Xu et al.   NATURE BIOTECHNOLOGY

The genome of the mesopolyploid crop species Brassica rapa

(2011) Xiaowu Wang et al.   NATURE GENETICS

Epoxycarotenoid cleavage by NCED5 fine-tunes ABA accumulation and affects seed dormancy and drought tolerance with other NCED family members

(2011) Anne Frey et al.   PLANT JOURNAL

Reduced expression of FatA thioesterases in Arabidopsis affects the oil content and fatty acid composition of the seeds

(2011) Antonio J. Moreno-Pérez et al.   PLANTA

Origins of the amphiploid species Brassica napus L. investigated by chloroplast and nuclear molecular markers

(2010) Charlotte J Allender et al.   BMC PLANT BIOLOGY

Population differentiation as a test for selective sweeps

(2010) H. Chen et al.   GENOME RESEARCH

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

(2010) A. McKenna et al.   GENOME RESEARCH

Arabidopsis  -Ketoacyl-[Acyl Carrier Protein] Synthase I Is Crucial for Fatty Acid Synthesis and Plays a Role in Chloroplast Division and Embryo Development

(2010) G.-Z. Wu et al.   PLANT CELL

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

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

Association of gene-linked SSR markers to seed glucosinolate content in oilseed rape (Brassica napus ssp. napus)

(2008) M. Hasan et al.   THEORETICAL AND APPLIED GENETICS