Genotyping-by-sequencing through transcriptomics: implementation in a range of crop species with varying reproductive habits and ploidy levels

Reference transcriptome assembly and annotation for perennial ryegrass

(2017) Hiroshi Shinozuka et al.   GENOME

Generation and Characterisation of a Reference Transcriptome for Phalaris (Phalaris aquatica L.)

(2017) Rebecca Baillie et al.   Agronomy-Basel

Elucidation of the genetic basis of variation for stem strength characteristics in bread wheat by Associative Transcriptomics

(2016) Charlotte N. Miller et al.   BMC GENOMICS

Efficiency of genomic selection for tomato fruit quality

(2016) Janejira Duangjit et al.   MOLECULAR BREEDING

Genomic Prediction of Testcross Performance in Canola (Brassica napus)

(2016) Habib U. Jan et al.   PLoS One

Changes in genetic selection differentials and generation intervals in US Holstein dairy cattle as a result of genomic selection

(2016) Adriana García-Ruiz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular markers for tolerance of European ash (Fraxinus excelsior) to dieback disease identified using Associative Transcriptomics

(2016) Andrea L. Harper et al.   Scientific Reports

Selection on Optimal Haploid Value Increases Genetic Gain and Preserves More Genetic Diversity Relative to Genomic Selection

(2015) Hans D. Daetwyler et al.   GENETICS

Single Nucleotide Polymorphism Identification in Polyploids: A Review, Example, and Recommendations

(2015) Josh Clevenger et al.   Molecular Plant

TheBrassica napusreceptor-like protein RLM2 is encoded by a second allele of theLepR3/Rlm2blackleg resistance locus

(2015) Nicholas J. Larkan et al.   PLANT BIOTECHNOLOGY JOURNAL

Rapid and Inexpensive Whole-Genome Genotyping-by-Sequencing for Crossover Localization and Fine-Scale Genetic Mapping

(2015) Beth A. Rowan et al.   G3-Genes Genomes Genetics

Genetic Gain from Phenotypic and Genomic Selection for Quantitative Resistance to Stem Rust of Wheat

(2015) J. Rutkoski et al.   Plant Genome

Genome-wide association mapping unravels the genetic control of seed germination and vigor in Brassica napus

(2015) Sarah V. Hatzig et al.   Frontiers in Plant Science

Selection on Optimal Haploid Value Increases Genetic Gain and Preserves More Genetic Diversity Relative to Genomic Selection

(2015) Hans D. Daetwyler et al.   GENETICS

Co-localisation of the blackleg resistance genes Rlm2 and LepR3 on Brassica napus chromosome A10

(2014) Nicholas J Larkan et al.   BMC PLANT BIOLOGY

Reduced representation approaches to interrogate genome diversity in large repetitive plant genomes

(2014) C. D. Hirsch et al.   Briefings in Functional Genomics

The sheep genome illuminates biology of the rumen and lipid metabolism

(2014) Y. Jiang et al.   SCIENCE

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

(2014) B. Chalhoub et al.   SCIENCE

Genomic selection in crops, trees and forages: a review

(2014) Z. Lin et al.   Crop & Pasture Science

Global RNA sequencing reveals that genotype-dependent allele-specific expression contributes to differential expression in rice F1 hybrids

(2013) Gaoyuan Song et al.   BMC PLANT BIOLOGY

StAMPP: an R package for calculation of genetic differentiation and structure of mixed-ploidy level populations

(2013) Luke W. Pembleton et al.   Molecular Ecology Resources

Development of Strategies for SNP Detection in RNA-Seq Data: Application to Lymphoblastoid Cell Lines and Evaluation Using 1000 Genomes Data

(2013) Emma M. Quinn et al.   PLoS One

Imputation of Unordered Markers and the Impact on Genomic Selection Accuracy

(2013) Jessica E. Rutkoski et al.   G3-Genes Genomes Genetics

Towards accurate detection and genotyping of expressed variants from whole transcriptome sequencing data

(2012) Jorge Duitama et al.   BMC GENOMICS

Using Tablet for visual exploration of second-generation sequencing data

(2012) I. Milne et al.   BRIEFINGS IN BIOINFORMATICS

Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture

(2012) N. Rohland et al.   GENOME RESEARCH

Analyses of pig genomes provide insight into porcine demography and evolution

(2012) Martien A. M. Groenen et al.   NATURE

Associative transcriptomics of traits in the polyploid crop species Brassica napus

(2012) Andrea L Harper et al.   NATURE BIOTECHNOLOGY

Genomic selection for growth and wood quality in Eucalyptus: capturing the missing heritability and accelerating breeding for complex traits in forest trees

(2012) Marcos D. V. Resende et al.   NEW PHYTOLOGIST

Targeted re-sequencing of the allohexaploid wheat exome

(2012) Mark O. Winfield et al.   PLANT BIOTECHNOLOGY JOURNAL

Genomic Selection for Fruit Quality Traits in Apple (Malus×domestica Borkh.)

(2012) Satish Kumar et al.   PLoS One

Differential Gene Expression in Soybean Leaf Tissues at Late Developmental Stages under Drought Stress Revealed by Genome-Wide Transcriptome Analysis

(2012) Dung Tien Le et al.   PLoS One

Genome-Wide Analysis of the World's Sheep Breeds Reveals High Levels of Historic Mixture and Strong Recent Selection

(2012) James W. Kijas et al.   PLOS BIOLOGY

A High-Throughput Method for Illumina RNA-Seq Library Preparation

(2012) Ravi Kumar et al.   Frontiers in Plant Science

Comparative visualization of genetic and physical maps with Strudel

(2011) M. Bayer et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by Illumina mRNA-Seq

(2011) Eshchar Mizrachi et al.   BMC GENOMICS

The development and characterization of a 60K SNP chip for chicken

(2011) Martien AM Groenen et al.   BMC GENOMICS

Targeted enrichment of genomic DNA regions for next-generation sequencing

(2011) F. Mertes et al.   Briefings in Functional Genomics

Dissecting the genome of the polyploid crop oilseed rape by transcriptome sequencing

(2011) Ian Bancroft et al.   NATURE BIOTECHNOLOGY

Genome-wide genetic marker discovery and genotyping using next-generation sequencing

(2011) John W. Davey et al.   NATURE REVIEWS GENETICS

Accelerating the domestication of trees using genomic selection: accuracy of prediction models across ages and environments

(2011) M. F. R. Resende et al.   NEW PHYTOLOGIST

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

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

Designing dairy cattle breeding schemes under genomic selection: a review of international research

(2011) J. E. Pryce et al.   Animal Production Science

The largest eukaryotic genome of them all?

(2010) JAUME PELLICER et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Genome sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

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

(2010) Xuehui Huang et al.   NATURE GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Global Analysis of Allele-Specific Expression in Arabidopsis thaliana

(2009) Xu Zhang et al.   GENETICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing

(2009) Andreas Gnirke et al.   NATURE BIOTECHNOLOGY

Single nucleotide polymorphism (SNP) discovery in the polyploidBrassica napususing Solexa transcriptome sequencing

(2009) Martin Trick et al.   PLANT BIOTECHNOLOGY JOURNAL

Development and Characterization of a High Density SNP Genotyping Assay for Cattle

(2009) Lakshmi K. Matukumalli et al.   PLoS One

Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology

(2009) Antonio M. Ramos et al.   PLoS One

The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

(2009) et al.   SCIENCE

Genome-wide allele-specific expression analysis using Massively Parallel Signature Sequencing (MPSS™) Reveals cis- and trans-effects on gene expression in maize hybrid meristem tissue

(2008) Mei Guo et al.   PLANT MOLECULAR BIOLOGY