Population genomic analyses from low-coverage RAD-Seq data: a case study on the non-model cucurbit bottle gourd

A RAD-based linkage map and comparative genomics in the gudgeons (genus Gnathopogon, Cyprinidae)

(2013) Ryo Kakioka et al.   BMC GENOMICS

De novo sequencing of sunflower genome for SNP discovery using RAD (Restriction site Associated DNA) approach

(2013) Venkatramana Pegadaraju et al.   BMC GENOMICS

Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing

(2013) R. Ogden et al.   MOLECULAR ECOLOGY

A resource of genome-wide single-nucleotide polymorphisms generated by RAD tag sequencing in the critically endangered European eel

(2013) J. M. Pujolar et al.   Molecular Ecology Resources

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

(2013) Rajeev K Varshney et al.   NATURE BIOTECHNOLOGY

Genotyping by RAD sequencing enables mapping of fatty acid composition traits in perennial ryegrass (Lolium perenne(L.))

(2013) Matthew Hegarty et al.   PLANT BIOTECHNOLOGY JOURNAL

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

Imputation of Unordered Markers and the Impact on Genomic Selection Accuracy

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

Association Mapping and the Genomic Consequences of Selection in Sunflower

(2013) Jennifer R. Mandel et al.   PLoS Genetics

Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol

(2013) Fei Lu et al.   PLoS Genetics

Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads

(2012) Z. Chong et al.   BIOINFORMATICS

Genetic map of Triticum turgidum based on a hexaploid wheat population without genetic recombination for D genome

(2012) Li Zhang et al.   BMC GENETICS

RAD tag sequencing as a source of SNP markers in Cynara cardunculus L

(2012) Davide Scaglione 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

Testing Hardy–Weinberg disequilibrium using the generalized linear model

(2012) SHIZHONG XU   Genetics Research

Genome-wide patterns of divergence and gene flow across a butterfly radiation

(2012) Nicola J. Nadeau et al.   MOLECULAR ECOLOGY

Molecular evolutionary and population genomic analysis of the nine-spined stickleback using a modified restriction-site-associated DNA tag approach

(2012) Matthieu Bruneaux et al.   MOLECULAR ECOLOGY

Genome sequence of dwarf birch (Betula nana) and cross-species RAD markers

(2012) Nian Wang et al.   MOLECULAR ECOLOGY

Special features of RAD Sequencing data: implications for genotyping

(2012) John W. Davey et al.   MOLECULAR ECOLOGY

Genome-wide association reveals genetic basis for the propensity to migrate in wild populations of rainbow and steelhead trout

(2012) Benjamin C. Hecht et al.   MOLECULAR ECOLOGY

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

(2012) Xuehui Huang et al.   NATURE

Genome-wide genetic changes during modern breeding of maize

(2012) Yinping Jiao et al.   NATURE GENETICS

The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions

(2012) Shaogui Guo et al.   NATURE GENETICS

Inferring Phylogenies from RAD Sequence Data

(2012) Benjamin E. R. Rubin et al.   PLoS One

Two Different High Throughput Sequencing Approaches Identify Thousands of De Novo Genomic Markers for the Genetically Depleted Bornean Elephant

(2012) Reeta Sharma et al.   PLoS One

The genome of melon (Cucumis melo L.)

(2012) J. Garcia-Mas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011) Eva-Maria Willing et al.   BIOINFORMATICS

Population- and genome-specific patterns of linkage disequilibrium and SNP variation in spring and winter wheat (Triticum aestivum L.)

(2011) Shiaoman Chao et al.   BMC GENOMICS

Partial sequencing of the bottle gourd genome reveals markers useful for phylogenetic analysis and breeding

(2011) Pei Xu et al.   BMC GENOMICS

Syntenic relationships between cucumber (Cucumis sativus L.) and melon (C. melo L.) chromosomes as revealed by comparative genetic mapping

(2011) Dawei Li 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

Multiple evidence for the role of an Ovate-like gene in determining fruit shape in pepper

(2011) Aphrodite Tsaballa et al.   BMC PLANT BIOLOGY

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges

(2011) S. J. HELYAR et al.   Molecular Ecology Resources

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

Distribution of SUN, OVATE, LC, and FAS in the Tomato Germplasm and the Relationship to Fruit Shape Diversity

(2011) G. R. Rodriguez et al.   PLANT PHYSIOLOGY

Increase in Tomato Locule Number Is Controlled by Two Single-Nucleotide Polymorphisms Located Near WUSCHEL

(2011) S. Munos et al.   PLANT PHYSIOLOGY

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

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

Linkage Mapping and Comparative Genomics Using Next-Generation RAD Sequencing of a Non-Model Organism

(2011) Simon W. Baxter et al.   PLoS One

Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne

(2011) W. F. Pfender et al.   THEORETICAL AND APPLIED GENETICS

Stacks : Building and Genotyping Loci De Novo From Short-Read Sequences

(2011) Julian M. Catchen et al.   G3-Genes Genomes Genetics

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

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

(2010) Paul A. Hohenlohe et al.   PLoS Genetics

SNP detection for massively parallel whole-genome resequencing

(2009) R. Li et al.   GENOME RESEARCH

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

(2009) R. Li et al.   GENOME RESEARCH

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

The genome of the cucumber, Cucumis sativus L.

(2009) Sanwen Huang et al.   NATURE GENETICS

Collection and morphological characterization of Lagenaria siceraria germplasm from the Mediterranean region of Turkey

(2008) H. Yetişir et al.   GENETIC RESOURCES AND CROP EVOLUTION

Regulatory change in YABBY-like transcription factor led to evolution of extreme fruit size during tomato domestication

(2008) Bin Cong et al.   NATURE GENETICS

Flow cytometric analysis in Lagenaria siceraria (Cucurbitaceae) indicates correlation of genome size with usage types and growing elevation

(2008) Enoch G. Achigan-Dako et al.   PLANT SYSTEMATICS AND EVOLUTION

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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

A Retrotransposon-Mediated Gene Duplication Underlies Morphological Variation of Tomato Fruit

(2008) H. Xiao et al.   SCIENCE