Resequencing of 683 common bean genotypes identifies yield component trait associations across a north–south cline

Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits

(2019) Rajeev K. Varshney et al.   NATURE GENETICS

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files

(2018) Chi Zhang et al.   BIOINFORMATICS

Natural variation at the soybean J locus improves adaptation to the tropics and enhances yield

(2017) Sijia Lu et al.   NATURE GENETICS

Whole-genome resequencing of 292 pigeonpea accessions identifies genomic regions associated with domestication and agronomic traits

(2017) Rajeev K Varshney et al.   NATURE GENETICS

Genome-Wide Association Study Identifies NBS-LRR-Encoding Genes Related with Anthracnose and Common Bacterial Blight in the Common Bean

(2017) Jing Wu et al.   Frontiers in Plant Science

Mapping and Genetic Structure Analysis of the Anthracnose Resistance Locus Co-1HY in the Common Bean (Phaseolus vulgaris L.)

(2017) Mingli Chen et al.   PLoS One

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

(2015) Zhengkui Zhou et al.   NATURE BIOTECHNOLOGY

A reference genome for common bean and genome-wide analysis of dual domestications

(2014) Jeremy Schmutz et al.   NATURE GENETICS

Fine mapping of Co-x, an anthracnose resistance gene to a highly virulent strain of Colletotrichum lindemuthianum in common bean

(2014) Manon M. S. Richard et al.   THEORETICAL AND APPLIED GENETICS

A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica)

(2013) Guanqing Jia et al.   NATURE GENETICS

GAPIT: genome association and prediction integrated tool

(2012) Alexander E. Lipka et al.   BIOINFORMATICS

The common bean growth habit gene PvTFL1y is a functional homolog of Arabidopsis TFL1

(2012) S. L. Repinski et al.   THEORETICAL AND APPLIED GENETICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data

(2011) Valentina Boeva et al.   BIOINFORMATICS

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

(2011) Xun Xu et al.   NATURE BIOTECHNOLOGY

STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method

(2011) Dent A. Earl et al.   Conservation Genetics Resources

GCTA: A Tool for Genome-wide Complex Trait Analysis

(2010) Jian Yang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Dominant gene for common bean resistance to common bacterial blight caused by Xanthomonas axonopodis pv. phaseoli

(2010) Mildred Zapata et al.   EUPHYTICA

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

(2010) A. McKenna et al.   GENOME RESEARCH

Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection

(2010) Hon-Ming Lam et al.   NATURE GENETICS

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Genetic mapping of microsatellite markers around the arcelin bruchid resistance locus in common bean

(2010) Matthew W. Blair et al.   THEORETICAL AND APPLIED GENETICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Local maternal control of seed size by KLUH/CYP78A5-dependent growth signaling

(2009) N. M. Adamski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Efficient Control of Population Structure in Model Organism Association Mapping

(2008) H. M. Kang et al.   GENETICS

Efficient Methods to Compute Genomic Predictions

(2008) P.M. VanRaden   JOURNAL OF DAIRY SCIENCE

Mapping Homologous Sequences for Determinacy and Photoperiod Sensitivity in Common Bean (Phaseolus vulgaris)

(2008) M. Kwak et al.   JOURNAL OF HEREDITY

Genetic diversity of Chinese common bean (Phaseolus vulgaris L.) landraces assessed with simple sequence repeat markers

(2008) Xiaoyan Zhang et al.   THEORETICAL AND APPLIED GENETICS