Sequencing consolidates molecular markers with plant breeding practice

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

(2014) Wolfgang Goettel et al.   BMC GENOMICS

Genomic analyses provide insights into the history of tomato breeding

(2014) Tao Lin et al.   NATURE GENETICS

Insights into RNA structure and function from genome-wide studies

(2014) Stefanie A. Mortimer et al.   NATURE REVIEWS GENETICS

A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

(2014) et al.   SCIENCE

New evidence of ancestral polyploidy in the Genistoid legume Lupinus angustifolius L. (narrow-leafed lupin)

(2014) Magdalena Kroc et al.   THEORETICAL AND APPLIED GENETICS

Genomic selection: genome-wide prediction in plant improvement

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

The Acid Phosphatase-Encoding Gene GmACP1 Contributes to Soybean Tolerance to Low-Phosphorus Stress

(2014) Dan Zhang et al.   PLoS Genetics

The past, present and future of breeding rust resistant wheat

(2014) Jeffrey G. Ellis et al.   Frontiers in Plant Science

CGtag: complete genomics toolkit and annotation in a cloud-based Galaxy

(2014) Saskia Hiltemann et al.   GigaScience

Genome wide SNP discovery in flax through next generation sequencing of reduced representation libraries

(2013) Santosh Kumar et al.   BMC GENOMICS

Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation

(2013) Judson A Ward 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

Development and validation of a PCR-based functional marker system for the brown planthopper resistance gene Bph14 in rice

(2013) Lei Zhou et al.   BREEDING SCIENCE

Sequence Analysis of the Genome of Carnation (Dianthus caryophyllus L.)

(2013) M. Yagi et al.   DNA RESEARCH

A procedure allowing up to eight generations of wheat and nine generations of barley per annum

(2013) Z. Zheng et al.   EUPHYTICA

Chromosomal location of genomic SSR markers associated with yellow rust resistance in Turkish bread wheat (Triticum aestivum L.)

(2013) F. SENTURK AKFIRAT et al.   JOURNAL OF GENETICS

Identification of SNP markers for inferring phylogeny in temperate bamboos (Poaceae: Bambusoideae) using RAD sequencing

(2013) X. Q. Wang et al.   Molecular Ecology Resources

Draft genome of the wheat A-genome progenitor Triticum urartu

(2013) Hong-Qing Ling et al.   NATURE

Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation

(2013) Jizeng Jia et al.   NATURE

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

(2013) Rajeev K Varshney et al.   NATURE BIOTECHNOLOGY

The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution

(2013) Ignazio Verde et al.   NATURE GENETICS

A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity

(2013) Jianjian Qi et al.   NATURE GENETICS

Draft Genome Sequence, and a Sequence-Defined Genetic Linkage Map of the Legume Crop Species Lupinus angustifolius L

(2013) Huaan Yang et al.   PLoS One

A Next-Generation Sequencing Method for Genotyping-by-Sequencing of Highly Heterozygous Autotetraploid Potato

(2013) Jan G. A. M. L. Uitdewilligen et al.   PLoS One

Dissecting yield-associated loci in super hybrid rice by resequencing recombinant inbred lines and improving parental genome sequences

(2013) Z.-Y. Gao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution

(2013) Jinfeng Chen et al.   Nature Communications

Sequence-Based Mapping of the Polyploid Wheat Genome

(2013) Cyrille Saintenac et al.   G3-Genes Genomes Genetics

Will genomic selection be a practical method for plant breeding?

(2012) Akihiro Nakaya et al.   ANNALS OF BOTANY

Sequence based polymorphic (SBP) marker technology for targeted genomic regions: its application in generating a molecular map of the Arabidopsis thaliana genome

(2012) Binod B Sahu et al.   BMC GENOMICS

Application of next-generation sequencing for rapid marker development in molecular plant breeding: a case study on anthracnose disease resistance in Lupinus angustifolius L.

(2012) Huaan Yang et al.   BMC GENOMICS

High-throughput polymorphism detection and genotyping in Brassica napus using next-generation RAD sequencing

(2012) Anja Bus et al.   BMC GENOMICS

Application of Genomic Tools in Plant Breeding

(2012) A. M. Perez-de-Castro et al.   CURRENT GENOMICS

On the Prospects of Whole-Genome Association Mapping in Saccharomyces cerevisiae

(2012) C. F. Connelly et al.   GENETICS

Short Communication Discovery of a large set of SNP and SSR genetic markers by high-throughput sequencing of pepper (Capsicum annuum)

(2012) M. Nicolaï et al.   GENETICS AND MOLECULAR RESEARCH

Whole-genome strategies for marker-assisted plant breeding

(2012) Yunbi Xu et al.   MOLECULAR BREEDING

Analysis of the bread wheat genome using whole-genome shotgun sequencing

(2012) Rachel Brenchley et al.   NATURE

Can genomics boost productivity of orphan crops?

(2012) Rajeev K Varshney 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

Maize HapMap2 identifies extant variation from a genome in flux

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

Development of a co-dominant DNA marker linked to the gene lentus conferring reduced pod shattering for marker-assisted selection in narrow-leafed lupin (Lupinus angustifolius) breeding

(2012) Xin Li et al.   PLANT BREEDING

Development of High-Density Genetic Maps for Barley and Wheat Using a Novel Two-Enzyme Genotyping-by-Sequencing Approach

(2012) Jesse A. Poland et al.   PLoS One

SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data

(2012) Rasmus Nielsen et al.   PLoS One

Tibet is one of the centers of domestication of cultivated barley

(2012) F. Dai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Rapid development of molecular markers by next-generation sequencing linked to a gene conferring phomopsis stem blight disease resistance for marker-assisted selection in lupin (Lupinus angustifolius L.) breeding

(2012) Huaan Yang et al.   THEORETICAL AND APPLIED GENETICS

Bridging the gap between genome analysis and precision breeding in potato

(2012) Christiane Gebhardt   TRENDS IN GENETICS

Cleavage and nuclear localization of the rice XA21 immune receptor

(2012) Chang-Jin Park et al.   Nature Communications

The genome of Prunus mume

(2012) Qixiang Zhang et al.   Nature Communications

Genomic Selection in Wheat Breeding using Genotyping-by-Sequencing

(2012) Jesse Poland et al.   Plant Genome

Paired-end RAD-seq for de novo assembly and marker design without available reference

(2011) Eva-Maria Willing et al.   BIOINFORMATICS

Identification of SNP and SSR markers in eggplant using RAD tag sequencing

(2011) Lorenzo Barchi et al.   BMC GENOMICS

Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley

(2011) Yada Chutimanitsakun et al.   BMC GENOMICS

Genomic selection in plant breeding: from theory to practice

(2011) J.-L. Jannink et al.   Briefings in Functional Genomics

Development of near-isogenic lines for a major QTL on 3BL conferring Fusarium crown rot resistance in hexaploid wheat

(2011) J. Ma et al.   EUPHYTICA

Multiplexed shotgun genotyping for rapid and efficient genetic mapping

(2011) P. Andolfatto et al.   GENOME RESEARCH

A molecular marker linked to the mollis gene conferring soft-seediness for marker-assisted selection applicable to a wide range of crosses in lupin (Lupinus angustifolius L.) breeding

(2011) Xin Li et al.   MOLECULAR BREEDING

Dynamo maker ready to roll

(2011) Susan Young   NATURE

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

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

(2011) Rajeev K Varshney et al.   NATURE BIOTECHNOLOGY

The genome of the mesopolyploid crop species Brassica rapa

(2011) Xiaowu Wang et al.   NATURE GENETICS

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

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

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

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

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

Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads

(2011) Paul D. Etter et al.   PLoS One

Molecular evidence for a single evolutionary origin of domesticated rice

(2011) J. Molina et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Development of a DNA marker tightly linked to low-alkaloid gene iucundus in narrow-leafed lupin (Lupinus angustifolius L.) for marker-assisted selection

(2011) X. Li et al.   Crop & Pasture Science

High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence

(2010) David L Hyten et al.   BMC GENOMICS

Molecular breeding in developing countries: challenges and perspectives

(2010) J-M Ribaut et al.   CURRENT OPINION IN PLANT BIOLOGY

Aligning a New Reference Genetic Map of Lupinus angustifolius with the Genome Sequence of the Model Legume, Lotus japonicus

(2010) M. N. Nelson et al.   DNA RESEARCH

Development of a co-dominant DNA marker tightly linked to gene tardus conferring reduced pod shattering in narrow-leafed lupin (Lupinus angustifolius L.)

(2010) Xin Li et al.   EUPHYTICA

Identification of a new fragrance allele in soybean and development of its functional marker

(2010) Ruangchai Juwattanasomran et al.   MOLECULAR BREEDING

Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines

(2010) Susanna Atwell et al.   NATURE

Genome sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

The genome of the domesticated apple (Malus × domestica Borkh.)

(2010) Riccardo Velasco et al.   NATURE GENETICS

Rice xa13 Recessive Resistance to Bacterial Blight Is Defeated by Induction of the Disease Susceptibility Gene Os-11N3

(2010) G. Antony et al.   PLANT CELL

Intragenic allele pyramiding combines different specificities of wheat Pm3 resistance alleles

(2010) Susanne Brunner et al.   PLANT 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

Resolving postglacial phylogeography using high-throughput sequencing

(2010) K. J. Emerson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Development of highly polymorphic SNP markers from the complexity reduced portion of maize [Zea mays L.] genome for use in marker-assisted breeding

(2010) Jafar A. Mammadov et al.   THEORETICAL AND APPLIED GENETICS

Crop genome sequencing: lessons and rationales

(2010) Catherine Feuillet et al.   TRENDS IN PLANT SCIENCE

Parallel and interlaced recurrent selection (PAIRS): Demonstration of the feasibility of implementing PAIRS to improve complete and partial resistance to blast (Magnaporthe grisea) and some other main traits in rice

(2009) Michel Vales et al.   FIELD CROPS RESEARCH

High-throughput genotyping by whole-genome resequencing

(2009) X. Huang et al.   GENOME RESEARCH

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Development of sequence-specific PCR markers associated with a polygenic controlled trait for marker-assisted selection using a modified selective genotyping strategy: a case study on anthracnose disease resistance in white lupin (Lupinus albus L.)

(2009) Huaan Yang et al.   MOLECULAR BREEDING

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

A First-Generation Haplotype Map of Maize

(2009) M. A. Gore et al.   SCIENCE

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

Next-generation sequencing technologies and their implications for crop genetics and breeding

(2009) Rajeev K. Varshney et al.   TRENDS IN BIOTECHNOLOGY

From mutations to MAGIC: resources for gene discovery, validation and delivery in crop plants

(2008) Colin Cavanagh et al.   CURRENT OPINION IN PLANT BIOLOGY

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Array-based high-throughput DNA markers for crop improvement

(2008) P K Gupta et al.   HEREDITY

Development of sequence-specific PCR markers linked to the Tardus gene that reduces pod shattering in narrow-leafed lupin (Lupinus angustifolius L.)

(2008) Jeffrey G. Boersma et al.   MOLECULAR BREEDING

Molecular Plant Breeding as the Foundation for 21st Century Crop Improvement

(2008) S. P. Moose et al.   PLANT PHYSIOLOGY

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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

Marker-assisted selection: an approach for precision plant breeding in the twenty-first century

(2007) B. C.Y Collard et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES