Expanding Omics Resources for Improvement of Soybean Seed Composition Traits

The CRISPR/Cas9 system for plant genome editing and beyond

(2015) Luisa Bortesi et al.   BIOTECHNOLOGY ADVANCES

Soybean (Glycine max) SWEET gene family: insights through comparative genomics, transcriptome profiling and whole genome re-sequence analysis

(2015) Gunvant Patil et al.   BMC GENOMICS

A systems biology approach toward understanding seed composition in soybean

(2015) Ling Li et al.   BMC GENOMICS

Gene expression profiling for seed protein and oil synthesis during early seed development in soybean

(2015) Young Eun Jang et al.   Genes & Genomics

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

(2015) Zhengkui Zhou et al.   NATURE BIOTECHNOLOGY

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

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

QTL for seed protein and amino acids in the Benning × Danbaekkong soybean population

(2015) C. V. Warrington et al.   THEORETICAL AND APPLIED GENETICS

Agricultural practices altered soybean seed protein, oil, fatty acids, sugars, and minerals in the Midsouth USA

(2015) Nacer Bellaloui et al.   Frontiers in Plant Science

Potential of Association Mapping and Genomic Selection to Explore PI 88788 Derived Soybean Cyst Nematode Resistance

(2015) Yong Bao et al.   Plant Genome

Legume genomics: understanding biology through DNA and RNA sequencing

(2014) Jamie A. O'Rourke et al.   ANNALS OF BOTANY

Expression quantitative trait loci infer the regulation of isoflavone accumulation in soybean (Glycine max L. Merr.) seed

(2014) Yan Wang et al.   BMC GENOMICS

Identification and characterization of transcript polymorphisms in soybean lines varying in oil composition and content

(2014) Wolfgang Goettel et al.   BMC GENOMICS

Genotyping by sequencing for genomic prediction in a soybean breeding population

(2014) Diego Jarquín et al.   BMC GENOMICS

SFGD: a comprehensive platform for mining functional information from soybean transcriptome data and its use in identifying acyl-lipid metabolism pathways

(2014) Juan Yu et al.   BMC GENOMICS

A genome-wide association study of seed protein and oil content in soybean

(2014) Eun-Young Hwang et al.   BMC GENOMICS

Deletions of the SACPD-C locus elevate seed stearic acid levels but also result in fatty acid and morphological alterations in nitrogen fixing nodules

(2014) Jason D Gillman et al.   BMC PLANT BIOLOGY

Translational Genomics in Agriculture: Some Examples in Grain Legumes

(2014) Rajeev K. Varshney et al.   CRITICAL REVIEWS IN PLANT SCIENCES

TraitCapture: genomic and environment modelling of plant phenomic data

(2014) Tim B Brown et al.   CURRENT OPINION IN PLANT BIOLOGY

Screening and identification of soybean seed-specific genes by using integrated bioinformatics of digital differential display, microarray, and RNA-seq data

(2014) Guangjun Yin et al.   GENE

Seed metabolomic study reveals significant metabolite variations and correlations among different soybean cultivars

(2014) Hong Lin et al.   Journal of Integrative Plant Biology

Metabolic map of mature maize kernels

(2014) Jun Rao et al.   Metabolomics

Assessing metabolomic and chemical diversity of a soybean lineage representing 35 years of breeding

(2014) Miyako Kusano et al.   Metabolomics

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

(2014) Ying-hui Li et al.   NATURE BIOTECHNOLOGY

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

(2014) Jeremy Schmutz et al.   NATURE GENETICS

Identification of loci governing eight agronomic traits using a GBS-GWAS approach and validation by QTL mapping in soya bean

(2014) Humira Sonah et al.   PLANT BIOTECHNOLOGY JOURNAL

Improved soybean oil quality by targeted mutagenesis of the fatty acid desaturase 2 gene family

(2014) William Haun et al.   PLANT BIOTECHNOLOGY JOURNAL

Quantitative trait loci analysis of soluble sugar contents in soybean

(2014) Yueqiang Wang et al.   PLANT BREEDING

Combined correlation-based network and mQTL analyses efficiently identified loci for branched-chain amino acid, serine to threonine, and proline metabolism in tomato seeds

(2014) David Toubiana et al.   PLANT JOURNAL

Targeted Genome Editing of Sweet Orange Using Cas9/sgRNA

(2014) Hongge Jia et al.   PLoS One

Genome Re-Sequencing of Semi-Wild Soybean Reveals a Complex Soja Population Structure and Deep Introgression

(2014) Jie Qiu et al.   PLoS One

Applying association mapping and genomic selection to the dissection of key traits in elite European wheat

(2014) Alison R. Bentley et al.   THEORETICAL AND APPLIED GENETICS

Genomic selection: genome-wide prediction in plant improvement

(2014) Zeratsion Abera Desta et al.   TRENDS IN PLANT SCIENCE

SoyFN: a knowledge database of soybean functional networks

(2014) Yungang Xu et al.   Database-The Journal of Biological Databases and Curation

The Genetic Architecture of Seed Composition in Soybean Is Refined by Genome-Wide Association Scans Across Multiple Populations

(2014) Justin N. Vaughn et al.   G3-Genes Genomes Genetics

Precision Genome Engineering and Agriculture: Opportunities and Regulatory Challenges

(2014) Daniel F. Voytas et al.   PLOS BIOLOGY

Soybean seed proteome rebalancing

(2014) Eliot M. Herman   Frontiers in Plant Science

Gel-free proteomic analysis of soybean root proteins affected by calcium under flooding stress

(2014) MyeongWon Oh et al.   Frontiers in Plant Science

Integrating omic approaches for abiotic stress tolerance in soybean

(2014) Rupesh Deshmukh et al.   Frontiers in Plant Science

Pheno-Copter: A Low-Altitude, Autonomous Remote-Sensing Robotic Helicopter for High-Throughput Field-Based Phenotyping

(2014) Scott Chapman et al.   Agronomy-Basel

Plant ionomics: a newer approach to study mineral transport and its regulation

(2013) Uma M. Singh et al.   ACTA PHYSIOLOGIAE PLANTARUM

Metabolomics for unknown plant metabolites

(2013) Ryo Nakabayashi et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Genomic differences between cultivated soybean, G. max and its wild relative G. soja

(2013) Trupti Joshi et al.   BMC GENOMICS

Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing

(2013) Ying-hui Li et al.   BMC GENOMICS

Potential assessment of genome-wide association study and genomic selection in Japanese pear Pyrus pyrifolia

(2013) Hiroyoshi Iwata et al.   BREEDING SCIENCE

Genetic Mapping and Confirmation of Quantitative Trait Loci for Seed Protein and Oil Contents and Seed Weight in Soybean

(2013) Safiullah M. Pathan et al.   CROP 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

Genomic selection of seed weight based on low-density SCAR markers in soybean

(2013) Y.J. Shu et al.   GENETICS AND MOLECULAR RESEARCH

Cross-validation in association mapping and its relevance for the estimation of QTL parameters of complex traits

(2013) T Würschum et al.   HEREDITY

Classification of Distinct Seed Carbohydrate Profiles in Soybean

(2013) Katherine B. Hagely et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Current metabolomics: Technological advances

(2013) Sastia P. Putri et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

Characterization of the fan1 locus in soybean line A5 and development of molecular assays for high-throughput genotyping of FAD3 genes

(2013) Anh-Tung Pham et al.   MOLECULAR BREEDING

Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement

(2013) Rajeev K Varshney et al.   NATURE BIOTECHNOLOGY

Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease

(2013) Vladimir Nekrasov et al.   NATURE BIOTECHNOLOGY

Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice

(2013) Wenzhi Jiang et al.   NUCLEIC ACIDS RESEARCH

Plant genome editing made easy: targeted mutagenesis in model and crop plants using the CRISPR/Cas system

(2013) Khaoula Belhaj et al.   Plant Methods

The advantages and limitations of trait analysis with GWAS: a review

(2013) Arthur Korte et al.   Plant Methods

Molecular characterization of Glycine max squalene synthase genes in seed phytosterol biosynthesis

(2013) Hanh T.M. Nguyen et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Development and Evaluation of SoySNP50K, a High-Density Genotyping Array for Soybean

(2013) Qijian Song et al.   PLoS One

An Improved Genotyping by Sequencing (GBS) Approach Offering Increased Versatility and Efficiency of SNP Discovery and Genotyping

(2013) Humira Sonah et al.   PLoS One

Analysis of Proteome Profile in Germinating Soybean Seed, and Its Comparison with Rice Showing the Styles of Reserves Mobilization in Different Crops

(2013) Chao Han et al.   PLoS One

Using RNA-Seq to Profile Soybean Seed Development from Fertilization to Maturity

(2013) Sarah I. Jones et al.   PLoS One

Genome-Wide Expression Analysis of Soybean MADS Genes Showing Potential Function in the Seed Development

(2013) Cheng-Ming Fan et al.   PLoS One

Comparison of SSR and SNP Markers in Estimation of Genetic Diversity and Population Structure of Indian Rice Varieties

(2013) Nivedita Singh et al.   PLoS One

Proteomic analysis of elite soybean Jidou17 and its parents using iTRAQ-based quantitative approaches

(2013) Jun Qin et al.   Proteome Science

BreedVision — A Multi-Sensor Platform for Non-Destructive Field-Based Phenotyping in Plant Breeding

(2013) Lucas Busemeyer et al.   SENSORS

Field high-throughput phenotyping: the new crop breeding frontier

(2013) José Luis Araus et al.   TRENDS IN PLANT SCIENCE

Assessment of Genetically Modified Soybean in Relation to Natural Variation in the Soybean Seed Metabolome

(2013) Joseph D. Clarke et al.   Scientific Reports

Legume Genomics: From Genomic Resources to Molecular Breeding

(2013) Rajeev K. Varshney et al.   Plant Genome

Proteomics: a biotechnology tool for crop improvement

(2013) Moustafa Eldakak et al.   Frontiers in Plant Science

NanoUPLC-MSE proteomic data assessment of soybean seeds using the Uniprot database

(2012) Andre M Murad et al.   BMC BIOTECHNOLOGY

Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics

(2012) Trupti Joshi et al.   BMC GENOMICS

Identification of soybean seed developmental stage-specific and tissue-specific miRNA targets by degradome sequencing

(2012) Md Shamimuzzaman et al.   BMC GENOMICS

Sequence mining and transcript profiling to explore differentially expressed genes associated with lipid biosynthesis during soybean seed development

(2012) Huan Chen et al.   BMC PLANT BIOLOGY

Environmental Stability of Oleic Acid Concentration in Seed Oil for Soybean Lines with and Mutant Genes

(2012) Jeong-Dong Lee et al.   CROP SCIENCE

Bromine, Chlorine, and Iodine Determination in Soybean and its Products by ICP-MS After Digestion Using Microwave-Induced Combustion

(2012) José Tiago Pereira Barbosa et al.   Food Analytical Methods

Ionome of Soybean Seed Affected by Previous Cropping with Mycorrhizal Plant and Manure Application

(2012) Zhimin Sha et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Improving metallomics information related to transgenic and non-transgenic soybean seeds using 2D-HPLC-ICP-MS and ESI-MS/MS

(2012) Lidiane Raquel Verola Mataveli et al.   Metallomics

Multi-environment mapping and meta-analysis of 100-seed weight in soybean

(2012) Ya-nan Sun et al.   MOLECULAR BIOLOGY REPORTS

Can genomics boost productivity of orphan crops?

(2012) Rajeev K Varshney et al.   NATURE BIOTECHNOLOGY

Dissection of genotype-phenotype associations in rice grains using metabolome quantitative trait loci analysis

(2012) Fumio Matsuda et al.   PLANT JOURNAL

Phosphoproteomic Analysis of Seed Maturation in Arabidopsis, Rapeseed, and Soybean

(2012) L. J. Meyer et al.   PLANT PHYSIOLOGY

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

(2012) Brant K. Peterson et al.   PLoS One

The Identification of Single Soybean Seed Variety by Laser Light Backscattering Imaging

(2012) Dazhou Zhu et al.   Sensor Letters

Combinations of mutant FAD2 and FAD3 genes to produce high oleic acid and low linolenic acid soybean oil

(2012) Anh-Tung Pham et al.   THEORETICAL AND APPLIED GENETICS

Genetic control of soybean seed oil: I. QTL and genes associated with seed oil concentration in RIL populations derived from crossing moderately high-oil parents

(2012) Mehrzad Eskandari et al.   THEORETICAL AND APPLIED GENETICS

Genotyping-by-Sequencing for Plant Breeding and Genetics

(2012) Jesse A. Poland et al.   Plant Genome

Ionomic Screening of Field-Grown Soybean Identifies Mutants with Altered Seed Elemental Composition

(2012) Greg Ziegler et al.   Plant Genome

An Integrated Quantitative Trait Locus Map of Oil Content in Soybean, Glycine max (L.) Merr., Generated Using a Meta-Analysis Method for Mining Genes

(2011) Zhao-ming QI et al.   Agricultural Sciences in China

New insights on proteomics of transgenic soybean seeds: evaluation of differential expressions of enzymes and proteins

(2011) Herbert S. Barbosa et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Genomic value prediction for quantitative traits under the epistatic model

(2011) Zhiqiu Hu et al.   BMC GENETICS

Combined analysis of transcriptome and metabolite data reveals extensive differences between black and brown nearly-isogenic soybean (Glycine max) seed coats enabling the identification of pigment isogenes

(2011) Nik Kovinich et al.   BMC GENOMICS

A meta-analysis of seed protein concentration QTL in soybean

(2011) Qi Zhao-ming et al.   CANADIAN JOURNAL OF PLANT SCIENCE

Soybean oil content QTL mapping and integrating with meta-analysis method for mining genes

(2011) Zhao-ming Qi et al.   EUPHYTICA

Large-scale sequencing of normalized full-length cDNA library of soybean seed at different developmental stages and analysis of the gene expression profiles based on ESTs

(2011) Ai-Hua Sha et al.   MOLECULAR BIOLOGY REPORTS

Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers

(2011) Rajeev K Varshney et al.   NATURE BIOTECHNOLOGY

Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting

(2011) Tomas Cermak et al.   NUCLEIC ACIDS RESEARCH

Metabolic engineering of soybean affords improved phytosterol seed traits

(2011) Anjanasree K. Neelakandan et al.   PLANT BIOTECHNOLOGY JOURNAL

Targeted Mutagenesis of Duplicated Genes in Soybean with Zinc-Finger Nucleases

(2011) S. J. Curtin et al.   PLANT PHYSIOLOGY

Silencing of Soybean Seed Storage Proteins Results in a Rebalanced Protein Composition Preserving Seed Protein Content without Major Collateral Changes in the Metabolome and Transcriptome

(2011) M. A. Schmidt et al.   PLANT PHYSIOLOGY

Global gene expression profiles in developing soybean seeds

(2011) Tomiko Asakura et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

(2011) Robert J. Elshire et al.   PLoS One

A novel FAD2-1 A allele in a soybean plant introduction offers an alternate means to produce soybean seed oil with 85% oleic acid content

(2011) Anh-Tung Pham et al.   THEORETICAL AND APPLIED GENETICS

Genomic Selection Accuracy using Multifamily Prediction Models in a Wheat Breeding Program

(2011) Elliot L. Heffner et al.   Plant Genome

Genome-wide association studies in plants: the missing heritability is in the field

(2011) Benjamin Brachi et al.   GENOME BIOLOGY

Flux of transcript patterns during soybean seed development

(2010) Sarah I Jones et al.   BMC GENOMICS

Mutant alleles of FAD2-1A and FAD2-1B combine to produce soybeans with the high oleic acid seed oil trait

(2010) Anh-Tung Pham et al.   BMC PLANT BIOLOGY

RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome

(2010) Andrew J Severin et al.   BMC PLANT BIOLOGY

Ionomics: The functional genomics of elements

(2010) I. Baxter   Briefings in Functional Genomics

Conditions Under Which Genome-Wide Association Studies Will be Positively Misleading

(2010) A. Platt et al.   GENETICS

Prediction of Genetic Values of Quantitative Traits in Plant Breeding Using Pedigree and Molecular Markers

(2010) J. Crossa et al.   GENETICS

A comparative study of element concentrations and binding in transgenic and non-transgenic soybean seeds

(2010) Lidiane Raquel Verola Mataveli et al.   Metallomics

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

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

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

Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA)

(2010) Jeffry D Sander et al.   NATURE METHODS

Developing of a simple method for screening soybean seedling cadmium accumulation to select soybean genotypes with low seed cadmium

(2010) Megumi Sugiyama et al.   PLANT AND SOIL

RNAi trigger fragment truncation attenuates soybean FAD2-1 transcript suppression and yields intermediate oil phenotypes

(2010) Nicholas Wagner et al.   PLANT BIOTECHNOLOGY JOURNAL

Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome

(2010) M. Y. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative analysis of soybean plasma membrane proteins under osmotic stress using gel-based and LC MS/MS-based proteomics approaches

(2010) Mohammad-Zaman Nouri et al.   PROTEOMICS

Rare Variants Create Synthetic Genome-Wide Associations

(2010) Samuel P. Dickson et al.   PLOS BIOLOGY

Metabolomics for Functional Genomics, Systems Biology, and Biotechnology

(2009) Kazuki Saito et al.   Annual Review of Plant Biology

New sources of soybean seed meal and oil composition traits identified through TILLING

(2009) Emily C Dierking et al.   BMC PLANT BIOLOGY

Soybean Proteome Database: A Data Resource for Plant Differential Omics

(2009) Katsumi Sakata et al.   JOURNAL OF PROTEOME RESEARCH

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

SoyBase, the USDA-ARS soybean genetics and genomics database

(2009) David Grant et al.   NUCLEIC ACIDS RESEARCH

Soybean Oil: Genetic Approaches for Modification of Functionality and Total Content

(2009) T. E. Clemente et al.   PLANT PHYSIOLOGY

Ionomics and the Study of the Plant Ionome

(2008) David E. Salt et al.   Annual Review of Plant Biology

SoyXpress: A database for exploring the soybean transcriptome

(2008) Kei Cheng et al.   BMC GENOMICS

Comparative metabolomic study of transgenic versus conventional soybean using capillary electrophoresis–time-of-flight mass spectrometry

(2008) Rocio García-Villalba et al.   JOURNAL OF CHROMATOGRAPHY A

In-Depth Investigation of the Soybean Seed-Filling Proteome and Comparison with a Parallel Study of Rapeseed

(2008) G. K. Agrawal et al.   PLANT PHYSIOLOGY

Expression of Umbelopsis ramanniana DGAT2A in Seed Increases Oil in Soybean

(2008) K. Lardizabal et al.   PLANT PHYSIOLOGY

Identification of differentially expressed genes in soybean seeds differing in oil content

(2008) Wen-Hui Wei et al.   PLANT SCIENCE

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One