Bulked sample analysis in genetics, genomics and crop improvement

Envirotyping for deciphering environmental impacts on crop plants

(2016) Yunbi Xu   THEORETICAL AND APPLIED GENETICS

Whole-genome resequencing: changing the paradigms of SNP detection, molecular mapping and gene discovery

(2015) Xiangyang Xu et al.   MOLECULAR BREEDING

Extreme-phenotype genome-wide association study (XP-GWAS): a method for identifying trait-associated variants by sequencing pools of individuals selected from a diversity panel

(2015) Jinliang Yang et al.   PLANT JOURNAL

Genetic mapping of the nulliplex-branch gene (gb_nb1) in cotton using next-generation sequencing

(2015) Wei Chen et al.   THEORETICAL AND APPLIED GENETICS

Identification of candidate genes associated with fertility restoration of cytoplasmic male-sterility in onion (Allium cepa L.) using a combination of bulked segregant analysis and RNA-seq

(2015) Sunggil Kim et al.   THEORETICAL AND APPLIED GENETICS

Application of in silico bulked segregant analysis for rapid development of markers linked to Bean common mosaic virus resistance in common bean

(2014) Marco H Bello et al.   BMC GENOMICS

A powerful tool for genome analysis in maize: development and evaluation of the high density 600 k SNP genotyping array

(2014) Sandra Unterseer et al.   BMC GENOMICS

Identification and characterization of nuclear genes involved in photosynthesis in Populus

(2014) Bowen Wang et al.   BMC PLANT BIOLOGY

Genomic prediction in biparental tropical maize populations in water-stressed and well-watered environments using low-density and GBS SNPs

(2014) X Zhang et al.   HEREDITY

Specific Oligopeptides in Fermented Soybean Extract Inhibit NF-κB-Dependent iNOS and Cytokine Induction by Toll-Like Receptor Ligands

(2014) Woo Hyung Lee et al.   JOURNAL OF MEDICINAL FOOD

Development of a SNP marker assay for the Lr67 gene of wheat using a genotyping by sequencing approach

(2014) Kerrie Forrest et al.   MOLECULAR BREEDING

Multiplex single-molecule interaction profiling of DNA-barcoded proteins

(2014) Liangcai Gu et al.   NATURE

Using next-generation sequencing to isolate mutant genes from forward genetic screens

(2014) Korbinian Schneeberger   NATURE REVIEWS GENETICS

Sequencing pools of individuals — mining genome-wide polymorphism data without big funding

(2014) Christian Schlötterer et al.   NATURE REVIEWS GENETICS

Discovery of rare mutations in extensively pooled DNA samples using multiple target enrichment

(2014) Xu Chi et al.   PLANT BIOTECHNOLOGY JOURNAL

RNA-Seq bulked segregant analysis enables the identification of high-resolution genetic markers for breeding in hexaploid wheat

(2014) Ricardo H. Ramirez-Gonzalez et al.   PLANT BIOTECHNOLOGY JOURNAL

Efficient Genome-Wide Detection and Cataloging of EMS-Induced Mutations Using Exome Capture and Next-Generation Sequencing

(2014) I. M. Henry et al.   PLANT CELL

Exploring Candidate Genes for Pericarp Russet Pigmentation of Sand Pear (Pyrus pyrifolia) via RNA-Seq Data in Two Genotypes Contrasting for Pericarp Color

(2014) Yue-zhi Wang et al.   PLoS One

Array-based proteomic approaches to study signal transduction pathways: Prospects, merits and challenges

(2014) Nikita Gahoi et al.   PROTEOMICS

Effects of MEK inhibitors GSK1120212 and PD0325901 in vivo using 10-plex quantitative proteomics and phosphoproteomics

(2014) Joao A. Paulo et al.   PROTEOMICS

Lr70, a new gene for leaf rust resistance mapped in common wheat accession KU3198

(2014) Colin W. Hiebert et al.   THEORETICAL AND APPLIED GENETICS

Combined use of bulked segregant analysis and microarrays reveals SNP markers pinpointing a major QTL for resistance to Phytophthora capsici in pepper

(2014) Wing-Yee Liu et al.   THEORETICAL AND APPLIED GENETICS

Next generation genetic mapping of the Ligon-lintless-2 (Li 2) locus in upland cotton (Gossypium hirsutum L.)

(2014) Gregory N. Thyssen et al.   THEORETICAL AND APPLIED GENETICS

QTL-seq identifies an early flowering QTL located near Flowering Locus T in cucumber

(2014) Hongfeng Lu et al.   THEORETICAL AND APPLIED GENETICS

A high-resolution linkage map of the Rfd1, a restorer-of-fertility locus for cytoplasmic male sterility in radish (Raphanus sativus L.) produced by a combination of bulked segregant analysis and RNA-Seq

(2014) Young-Pyo Lee et al.   THEORETICAL AND APPLIED GENETICS

Genotype × environment interaction QTL mapping in plants: lessons from Arabidopsis

(2014) Mohamed El-Soda et al.   TRENDS IN PLANT SCIENCE

Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding

(2014) Jiangfeng He et al.   Frontiers in Plant Science

Protein microarray technology: how far off is routine diagnostics?

(2013) Marina Cretich et al.   ANALYST

BSTA: a targeted approach combines bulked segregant analysis with next- generation sequencing and de novo transcriptome assembly for SNP discovery in sunflower

(2013) Maren Livaja et al.   BMC GENOMICS

Fine mapping of the uniform immature fruit color gene u in cucumber (Cucumis sativus L.)

(2013) Xuqin Yang et al.   EUPHYTICA

Positional cloning of the rice male sterility gene ms-IR36, widely used in the inter-crossing phase of recurrent selection schemes

(2013) Julien Frouin et al.   MOLECULAR BREEDING

Assessment of transcript reconstruction methods for RNA-seq

(2013) Tamara Steijger et al.   NATURE METHODS

Discovery of protein interactions using parallel analysis of translated ORFs (PLATO)

(2013) H Benjamin Larman et al.   Nature Protocols

MutMap-Gap: whole-genome resequencing of mutant F2 progeny bulk combined withde novoassembly of gap regions identifies the rice blast resistance genePii

(2013) Hiroki Takagi et al.   NEW PHYTOLOGIST

QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations

(2013) Hiroki Takagi et al.   PLANT JOURNAL

Identifying Genotype-by-Environment Interactions in the Metabolism of Germinating Arabidopsis Seeds Using Generalized Genetical Genomics

(2013) R. V. L. Joosen et al.   PLANT PHYSIOLOGY

Genotyping-by-Sequencing (GBS): A Novel, Efficient and Cost-Effective Genotyping Method for Cattle Using Next-Generation Sequencing

(2013) Marcos De Donato et al.   PLoS One

Mapping of Quantitative Trait Loci Underlying Cold Tolerance in Rice Seedlings via High-Throughput Sequencing of Pooled Extremes

(2013) Zemao Yang et al.   PLoS One

The genomic determinants of genotype × environment interactions in gene expression

(2013) Vladislav Grishkevich et al.   TRENDS IN GENETICS

Field high-throughput phenotyping: the new crop breeding frontier

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

RNA sequencing reveals the complex regulatory network in the maize kernel

(2013) Junjie Fu et al.   Nature Communications

A six-plex proteome quantification strategy reveals the dynamics of protein turnover

(2013) Fangjun Wang et al.   Scientific Reports

A Rapid, Direct, Quantitative, and Label-Free Detector of Cardiac Biomarker Troponin T Using Near-Infrared Fluorescent Single-Walled Carbon Nanotube Sensors

(2013) Jingqing Zhang et al.   Advanced Healthcare Materials

A Genome-Wide, Fine-Scale Map of Natural Pigmentation Variation in Drosophila melanogaster

(2013) Héloïse Bastide et al.   PLoS Genetics

Comparative Genomic and Functional Analysis of 100 Lactobacillus rhamnosus Strains and Their Comparison with Strain GG

(2013) François P. Douillard et al.   PLoS Genetics

Evaluation and Bulked Segregant Analysis of Major Yield QTL qtl12.1 Introgressed into Indigenous Elite Line for Low Water Availability under Water Stress

(2013) N. Manikanda BOOPATHI et al.   Rice Science

Effects of abiotic stress on plants: a systems biology perspective

(2012) Grant R Cramer et al.   BMC PLANT BIOLOGY

Combining SNP discovery from next-generation sequencing data with bulked segregant analysis (BSA) to fine-map genes in polyploid wheat

(2012) Martin Trick et al.   BMC PLANT BIOLOGY

Deciphering and Prediction of Transcriptome Dynamics under Fluctuating Field Conditions

(2012) Atsushi J. Nagano et al.   CELL

Bulk segregant analysis: “An effective approach for mapping consistent-effect drought grain yield QTLs in rice”

(2012) Prashant Vikram et al.   FIELD CROPS RESEARCH

Development of TILLING by sequencing platform towards enhanced leaf yield in tobacco

(2012) Thamalampudi Venkata Reddy et al.   INDUSTRIAL CROPS AND PRODUCTS

Metabolite profiling and quantitative genetics of natural variation for flavonoids in Arabidopsis

(2012) Jean-Marc Routaboul et al.   JOURNAL OF EXPERIMENTAL BOTANY

Cloning, In Silico Characterization and Prediction of Three Dimensional Structure of SbDof1, SbDof19, SbDof23 and SbDof24 Proteins from Sorghum [Sorghum bicolor (L.) Moench]

(2012) Hariom Kushwaha et al.   MOLECULAR BIOTECHNOLOGY

Whole-genome strategies for marker-assisted plant breeding

(2012) Yunbi Xu et al.   MOLECULAR BREEDING

Genome sequencing reveals agronomically important loci in rice using MutMap

(2012) Akira Abe et al.   NATURE BIOTECHNOLOGY

Comparative population genomics of maize domestication and improvement

(2012) Matthew B Hufford et al.   NATURE GENETICS

Genome-wide genetic changes during modern breeding of maize

(2012) Yinping Jiao et al.   NATURE GENETICS

Genomic and metabolic prediction of complex heterotic traits in hybrid maize

(2012) Christian Riedelsheimer et al.   NATURE GENETICS

Among- and within-population variation in flowering time of IberianArabidopsis thalianaestimated in field and glasshouse conditions

(2012) Belén Méndez-Vigo et al.   NEW PHYTOLOGIST

Root-lodging resistance in maize as an example for high-throughput genetic mapping via single nucleotide polymorphism-based selective genotyping

(2012) Mohammad Farkhari et al.   PLANT BREEDING

Gene Mapping via Bulked Segregant RNA-Seq (BSR-Seq)

(2012) Sanzhen Liu et al.   PLoS One

Population genomic and genome-wide association studies of agroclimatic traits in sorghum

(2012) G. P. Morris et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Development of a multiple bulked segregant analysis (MBSA) method used to locate a new stem rust resistance gene (Sr54) in the winter wheat cultivar Norin 40

(2012) Habibollah Ghazvini et al.   THEORETICAL AND APPLIED GENETICS

Genotyping-by-Sequencing for Plant Breeding and Genetics

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

Phenotyping for drought tolerance of crops in the genomics era

(2012) Roberto Tuberosa   Frontiers in Physiology

Analytical Aspects of Proteomics: 2009–2010

(2011) Zhibin Ning et al.   ANALYTICAL CHEMISTRY

Label-free analysis of biomolecular interactions using SPR imaging

(2011) Voula Kodoyianni   BIOTECHNIQUES

qDTY1.1, a major QTL for rice grain yield under reproductive-stage drought stress with a consistent effect in multiple elite genetic backgrounds

(2011) Prashant Vikram et al.   BMC GENETICS

Antibody Colocalization Microarray: A Scalable Technology for Multiplex Protein Analysis in Complex Samples

(2011) M. Pla-Roca et al.   MOLECULAR & CELLULAR PROTEOMICS

Identification of Quantitative Trait Loci for Lipid Metabolism in Rice Seeds

(2011) Jie-Zheng Ying et al.   Molecular Plant

A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease

(2011) Terri A Addona et al.   NATURE BIOTECHNOLOGY

A targeted proteomics–based pipeline for verification of biomarkers in plasma

(2011) Jeffrey R Whiteaker et al.   NATURE BIOTECHNOLOGY

Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm

(2011) Xuehui Huang et al.   NATURE GENETICS

Characterization of metabolite quantitative trait loci and metabolic networks that control glucosinolate concentration in the seeds and leaves of Brassica napus

(2011) Ji Feng et al.   NEW PHYTOLOGIST

ArabidopsisRTNLB1 and RTNLB2 Reticulon-Like Proteins Regulate Intracellular Trafficking and Activity of the FLS2 Immune Receptor

(2011) Hyoung Yool Lee et al.   PLANT CELL

Systematic knockdown of morphine pathway enzymes in opium poppy using virus-induced gene silencing

(2011) Champa P. Wijekoon et al.   PLANT JOURNAL

Next-generation mapping of Arabidopsis genes

(2011) Ryan S. Austin et al.   PLANT JOURNAL

Bulk Segregant Analysis Using Single Nucleotide Polymorphism Microarrays

(2011) Anthony Becker et al.   PLoS One

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

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

A Large Maize (Zea mays L.) SNP Genotyping Array: Development and Germplasm Genotyping, and Genetic Mapping to Compare with the B73 Reference Genome

(2011) Martin W. Ganal et al.   PLoS One

Deciphering the complexities of the wheat flour proteome using quantitative two-dimensional electrophoresis, three proteases and tandem mass spectrometry

(2011) Frances M Dupont et al.   Proteome Science

Adaptation to Climate Across the Arabidopsis thaliana Genome

(2011) A. M. Hancock et al.   SCIENCE

Combining Genome-Wide Association Mapping and Transcriptional Networks to Identify Novel Genes Controlling Glucosinolates in Arabidopsis thaliana

(2011) Eva K. F. Chan et al.   PLOS BIOLOGY

The Statistics of Bulk Segregant Analysis Using Next Generation Sequencing

(2011) Paul M. Magwene et al.   PLoS Computational Biology

Genome-Wide Association Study Using Extreme Truncate Selection Identifies Novel Genes Affecting Bone Mineral Density and Fracture Risk

(2011) Emma L. Duncan et al.   PLoS Genetics

Design of association studies with pooled or un-pooled next-generation sequencing data

(2010) Su Yeon Kim et al.   GENETIC EPIDEMIOLOGY

Two-dimensional gel electrophoresis in proteomics: Past, present and future

(2010) Thierry Rabilloud et al.   Journal of Proteomics

Genome wide identification of Dof transcription factor gene family in sorghum and its comparative phylogenetic analysis with rice and Arabidopsis

(2010) Hariom Kushwaha et al.   MOLECULAR BIOLOGY REPORTS

Nuclear proteomic changes linked to soybean rust resistance

(2010) Bret Cooper et al.   Molecular BioSystems

Efficiency of selective genotyping for genetic analysis of complex traits and potential applications in crop improvement

(2010) Yanping Sun et al.   MOLECULAR BREEDING

Dissection of genetically complex traits with extremely large pools of yeast segregants

(2010) Ian M. Ehrenreich et al.   NATURE

Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils

(2010) Thomas L Turner et al.   NATURE GENETICS

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

(2010) Xuehui Huang et al.   NATURE GENETICS

Mass spectrometry in high-throughput proteomics: ready for the big time

(2010) Tommy Nilsson et al.   NATURE METHODS

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

Identification of salt responsive genes using comparative microarray analysis in Upland cotton (Gossypium hirsutum L.)

(2010) Laura Rodriguez-Uribe et al.   PLANT SCIENCE

Linkage and Association Mapping of Arabidopsis thaliana Flowering Time in Nature

(2010) Benjamin Brachi et al.   PLoS Genetics

Bulked Segregant Analysis to Detect QTL Related to Heat Tolerance in Rice (Oryza sativa L.) Using SSR Markers

(2009) Gui-lian ZHANG et al.   Agricultural Sciences in China

2-DE with IPGs

(2009) Angelika Görg et al.   ELECTROPHORESIS

High-Throughput Genetic Mapping of Mutants via Quantitative Single Nucleotide Polymorphism Typing

(2009) S. Liu et al.   GENETICS

High-throughput genotyping by whole-genome resequencing

(2009) X. Huang et al.   GENOME RESEARCH

High-throughput SNP genotyping with the GoldenGate assay in maize

(2009) Jianbing Yan et al.   MOLECULAR BREEDING

Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma

(2009) Terri A Addona et al.   NATURE BIOTECHNOLOGY

System-wide molecular evidence for phenotypic buffering in Arabidopsis

(2009) Jingyuan Fu et al.   NATURE GENETICS

SHOREmap: simultaneous mapping and mutation identification by deep sequencing

(2009) Korbinian Schneeberger et al.   NATURE METHODS

A Multiparent Advanced Generation Inter-Cross to Fine-Map Quantitative Traits in Arabidopsis thaliana

(2009) Paula X. Kover et al.   PLoS Genetics

In situ synthesis of protein arrays

(2008) Mingyue He et al.   CURRENT OPINION IN BIOTECHNOLOGY

MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays

(2008) S. C. Popescu et al.   GENES & DEVELOPMENT

Genetic Design and Statistical Power of Nested Association Mapping in Maize

(2008) Jianming Yu et al.   GENETICS

Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast

(2008) Lyris M. F. de Godoy et al.   NATURE

Printing protein arrays from DNA arrays

(2008) Mingyue He et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Highly cost-efficient genome-wide association studies using DNA pools and dense SNP arrays

(2008) S. Macgregor et al.   NUCLEIC ACIDS RESEARCH

Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology

(2008) Richard Cronn et al.   NUCLEIC ACIDS RESEARCH

Minitags for small molecules: detecting targets of reactive small molecules in living plant tissues using ‘click chemistry’

(2008) Farnusch Kaschani et al.   PLANT JOURNAL

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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

QTL detection with bidirectional and unidirectional selective genotyping: marker-based and trait-based analyses

(2008) Alizera Navabi et al.   THEORETICAL AND APPLIED GENETICS

Developing and evaluating complex interventions: the new Medical Research Council guidance

(2008) Peter Craig et al.   BMJ-British Medical Journal