The patterns of deleterious mutations during the domestication of soybean

Dominance Effects and Functional Enrichments Improve Prediction of Agronomic Traits in Hybrid Maize

(2020) Guillaume P. Ramstein et al.   GENETICS

Pan-Genome of Wild and Cultivated Soybeans

(2020) Yucheng Liu et al.   CELL

Genetic dissection of domestication-related traits in soybean through genotyping-by-sequencing of two interspecific mapping populations

(2019) Stephen A. Swarm et al.   THEORETICAL AND APPLIED GENETICS

Genome-wide association study of seed protein, oil and amino acid contents in soybean from maturity groups I to IV

(2019) Sungwoo Lee et al.   THEORETICAL AND APPLIED GENETICS

Historical Meiotic Crossover Hotspots Fueled Patterns of Evolutionary Divergence in Rice

(2019) Alexandre P. Marand et al.   PLANT CELL

Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome

(2019) Fei He et al.   NATURE GENETICS

Chromosomal features revealed by comparison of genetic maps of Glycine max and Glycine soja

(2019) Kwanghee Lee et al.   GENOMICS

Natural variation and selection in GmSWEET39 affect soybean seed oil content

(2019) Long Miao et al.   NEW PHYTOLOGIST

Imputation of 3 million SNPs in the Arabidopsis regional mapping population

(2019) Bader Arouisse et al.   PLANT JOURNAL

The Rise and Fall of African Rice Cultivation Revealed by Analysis of 246 New Genomes

(2018) Philippe Cubry et al.   CURRENT BIOLOGY

A One-Penny Imputed Genome from Next-Generation Reference Panels

(2018) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Genomic variation in 3,010 diverse accessions of Asian cultivated rice

(2018) Wensheng Wang et al.   NATURE

An imputation platform to enhance integration of rice genetic resources

(2018) Diane R. Wang et al.   Nature Communications

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

(2018) Chi Zhang et al.   BIOINFORMATICS

Genetic diversity patterns and domestication origin of soybean

(2018) Soon-Chun Jeong et al.   THEORETICAL AND APPLIED GENETICS

Genetic Costs of Domestication and Improvement

(2017) Brook T Moyers et al.   JOURNAL OF HEREDITY

Signatures of local adaptation in lowland and highland teosintes from whole-genome sequencing of pooled samples

(2017) M.-A. Fustier et al.   MOLECULAR ECOLOGY

A chromosome conformation capture ordered sequence of the barley genome

(2017) Martin Mascher et al.   NATURE

Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation

(2017) Punna Ramu et al.   NATURE GENETICS

An xQTL map integrates the genetic architecture of the human brain's transcriptome and epigenome

(2017) Bernard Ng et al.   NATURE NEUROSCIENCE

Codon optimality, bias and usage in translation and mRNA decay

(2017) Gavin Hanson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Evolutionary genomics of grape (Vitis viniferassp.vinifera) domestication

(2017) Yongfeng Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular mapping and genomics of soybean seed protein: a review and perspective for the future

(2017) Gunvant Patil et al.   THEORETICAL AND APPLIED GENETICS

The Evolutionary Interplay between Adaptation and Self-Fertilization

(2017) Matthew Hartfield et al.   TRENDS IN GENETICS

Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize

(2017) Jinliang Yang et al.   PLoS Genetics

Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01

(2016) Qijian Song et al.   BMC GENOMICS

Preferential use of minor codons in the translation initiation region of human genes

(2016) Jung-Ho Park et al.   HUMAN GENETICS

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Role of Deleterious Substitutions in Crop Genomes

(2016) Thomas J. Y. Kono et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

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

Genome-wide association study using whole-genome sequencing rapidly identifies new genes influencing agronomic traits in rice

(2016) Kenji Yano et al.   NATURE GENETICS

Domestication history and geographical adaptation inferred from a SNP map of African rice

(2016) Rachel S Meyer et al.   NATURE GENETICS

Landscape of genomic diversity and trait discovery in soybean

(2016) Babu Valliyodan et al.   Scientific Reports

New Software for the Fast Estimation of Population Recombination Rates (FastEPRR) in the Genomic Era

(2016) Feng Gao et al.   G3-Genes Genomes Genetics

Full-genome evolutionary histories of selfing, splitting, and selection inCaenorhabditis

(2015) Cristel G. Thomas et al.   GENOME RESEARCH

The Accumulation of Deleterious Mutations as a Consequence of Domestication and Improvement in Sunflowers and Other Compositae Crops

(2015) Sebastien Renaut et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2015) Zhengkui Zhou et al.   NATURE BIOTECHNOLOGY

Excess of rare, inherited truncating mutations in autism

(2015) Niklas Krumm et al.   NATURE GENETICS

Genetic variance estimation with imputed variants finds negligible missing heritability for human height and body mass index

(2015) Jian Yang et al.   NATURE GENETICS

SIFT missense predictions for genomes

(2015) Robert Vaser et al.   Nature Protocols

Development, validation and genetic analysis of a large soybean SNP genotyping array

(2015) Yun-Gyeong Lee et al.   PLANT JOURNAL

Recombination in diverse maize is stable, predictable, and associated with genetic load

(2015) Eli Rodgers-Melnick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs

(2015) Clare D. Marsden et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Distance from sub-Saharan Africa predicts mutational load in diverse human genomes

(2015) Brenna M. Henn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of haplotypes at the Rsv4 genomic region in soybean associated with durable resistance to soybean mosaic virus

(2015) Daniel C. Ilut et al.   THEORETICAL AND APPLIED GENETICS

Fingerprinting Soybean Germplasm and Its Utility in Genomic Research

(2015) Qijian Song et al.   G3-Genes Genomes Genetics

A Population Structure and Genome-Wide Association Analysis on the USDA Soybean Germplasm Collection

(2015) Nonoy Bandillo et al.   Plant Genome

fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets

(2014) Anil Raj et al.   GENETICS

The deleterious mutation load is insensitive to recent population history

(2014) Yuval B Simons et al.   NATURE GENETICS

Common Genetic Variants Modulate Pathogen-Sensing Responses in Human Dendritic Cells

(2014) M. N. Lee et al.   SCIENCE

Population Structure and Domestication Revealed by High-Depth Resequencing of Korean Cultivated and Wild Soybean Genomes

(2013) W.-H. Chung et al.   DNA RESEARCH

Conservation and Functional Element Discovery in 20 Angiosperm Plant Genomes

(2013) D. Hupalo et al.   MOLECULAR BIOLOGY AND EVOLUTION

Three keys to the radiation of angiosperms into freezing environments

(2013) Amy E. Zanne et al.   NATURE

Genome-Wide Association Study and Pathway-Level Analysis of Tocochromanol Levels in Maize Grain

(2013) Alexander E. Lipka et al.   G3-Genes Genomes Genetics

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

(2012) Xuehui Huang et al.   NATURE

Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants

(2012) Wenqing Fu et al.   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Comparative population genomics of maize domestication and improvement

(2012) Matthew B Hufford et al.   NATURE GENETICS

Maize HapMap2 identifies extant variation from a genome in flux

(2012) Jer-Ming Chia et al.   NATURE GENETICS

An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations

(2012) Vincent Segura et al.   NATURE GENETICS

Genome-wide efficient mixed-model analysis for association studies

(2012) Xiang Zhou et al.   NATURE GENETICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

Genome-wide association study of leaf architecture in the maize nested association mapping population

(2011) Feng Tian et al.   NATURE GENETICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Archaeological Soybean (Glycine max) in East Asia: Does Size Matter?

(2011) Gyoung-Ah Lee et al.   PLoS One

GCTA: A Tool for Genome-wide Complex Trait Analysis

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

Population differentiation as a test for selective sweeps

(2010) H. Chen et al.   GENOME RESEARCH

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

Genome-wide association studies of 14 agronomic traits in rice landraces

(2010) Xuehui Huang et al.   NATURE GENETICS

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

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

Data quality control in genetic case-control association studies

(2010) Carl A Anderson et al.   Nature Protocols

The Composition and Origins of Genomic Variation among Individuals of the Soybean Reference Cultivar Williams 82

(2010) W. J. Haun et al.   PLANT PHYSIOLOGY

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

(2010) Eugene V. Davydov et al.   PLoS Computational Biology

A Unified Approach to Genotype Imputation and Haplotype-Phase Inference for Large Data Sets of Trios and Unrelated Individuals

(2009) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

The genetics of inbreeding depression

(2009) Deborah Charlesworth et al.   NATURE REVIEWS GENETICS

SoyBase, the USDA-ARS soybean genetics and genomics database

(2009) David Grant et al.   NUCLEIC ACIDS RESEARCH

A First-Generation Haplotype Map of Maize

(2009) M. A. Gore et al.   SCIENCE