Published in PLoS Genet on January 17, 2013
TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline. PLoS One (2014) 3.45
Comprehensive genotyping of the USA national maize inbred seed bank. Genome Biol (2013) 2.46
Classification and characterization of species within the genus lens using genotyping-by-sequencing (GBS). PLoS One (2015) 1.46
Fast and cost-effective genetic mapping in apple using next-generation sequencing. G3 (Bethesda) (2014) 1.44
An evaluation of genotyping by sequencing (GBS) to map the Breviaristatum-e (ari-e) locus in cultivated barley. BMC Genomics (2014) 1.37
Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley. PLoS One (2013) 1.30
Construction of a SNP-based genetic linkage map in cultivated peanut based on large scale marker development using next-generation double-digest restriction-site-associated DNA sequencing (ddRADseq). BMC Genomics (2014) 1.30
Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding. Front Plant Sci (2014) 1.26
Using genotyping-by-sequencing (GBS) for genomic discovery in cultivated oat. PLoS One (2014) 1.23
Genomic prediction in biparental tropical maize populations in water-stressed and well-watered environments using low-density and GBS SNPs. Heredity (Edinb) (2014) 1.10
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A footprint of past climate change on the diversity and population structure of Miscanthus sinensis. Ann Bot (2014) 1.10
A saturated genetic linkage map of autotetraploid alfalfa (Medicago sativa L.) developed using genotyping-by-sequencing is highly syntenous with the Medicago truncatula genome. G3 (Bethesda) (2014) 1.10
Genotyping by genome reducing and sequencing for outbred animals. PLoS One (2013) 1.00
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Prediction accuracies for growth and wood attributes of interior spruce in space using genotyping-by-sequencing. BMC Genomics (2015) 0.90
Defining loci in restriction-based reduced representation genomic data from nonmodel species: sources of bias and diagnostics for optimal clustering. Biomed Res Int (2014) 0.89
DNA fingerprinting in botany: past, present, future. Investig Genet (2014) 0.89
Genotyping-by-sequencing for Populus population genomics: an assessment of genome sampling patterns and filtering approaches. PLoS One (2014) 0.88
Genome-wide association study based on multiple imputation with low-depth sequencing data: application to biofuel traits in reed canarygrass. G3 (Bethesda) (2015) 0.88
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Genetic structure of Miscanthus sinensis and Miscanthus sacchariflorus in Japan indicates a gradient of bidirectional but asymmetric introgression. J Exp Bot (2015) 0.86
Comparative genomic analysis of the R2R3 MYB secondary cell wall regulators of Arabidopsis, poplar, rice, maize, and switchgrass. BMC Plant Biol (2014) 0.86
Construction of relatedness matrices using genotyping-by-sequencing data. BMC Genomics (2015) 0.86
Heterozygous Mapping Strategy (HetMappS) for High Resolution Genotyping-By-Sequencing Markers: A Case Study in Grapevine. PLoS One (2015) 0.86
Population genomic variation reveals roles of history, adaptation and ploidy in switchgrass. Mol Ecol (2014) 0.86
A high-density linkage map for Astyanax mexicanus using genotyping-by-sequencing technology. G3 (Bethesda) (2014) 0.85
Genotyping by sequencing approaches to characterise crop genomes: choosing the right tool for the right application. Plant Biotechnol J (2016) 0.85
Spiked GBS: a unified, open platform for single marker genotyping and whole-genome profiling. BMC Genomics (2015) 0.84
Construction of high-quality recombination maps with low-coverage genomic sequencing for joint linkage analysis in maize. BMC Biol (2015) 0.84
Using Mendelian inheritance to improve high-throughput SNP discovery. Genetics (2014) 0.84
Accelerating the switchgrass (Panicum virgatum L.) breeding cycle using genomic selection approaches. PLoS One (2014) 0.84
Accuracy of genomic selection for alfalfa biomass yield in different reference populations. BMC Genomics (2015) 0.83
Ecological characteristics and in situ genetic associations for yield-component traits of wild Miscanthus from eastern Russia. Ann Bot (2016) 0.83
Molecular characterization of CIMMYT maize inbred lines with genotyping-by-sequencing SNPs. Theor Appl Genet (2016) 0.83
Population genomics of pearl millet (Pennisetum glaucum (L.) R. Br.): Comparative analysis of global accessions and Senegalese landraces. BMC Genomics (2015) 0.83
Switchgrass (Panicum virgatum L.) Genotypes Differ between Coastal Sites and Inland Road Corridors in the Northeastern US. PLoS One (2015) 0.82
Identification of SNP and SSR Markers in Finger Millet Using Next Generation Sequencing Technologies. PLoS One (2016) 0.82
Genotyping-By-Sequencing (GBS) Detects Genetic Structure and Confirms Behavioral QTL in Tame and Aggressive Foxes (Vulpes vulpes). PLoS One (2015) 0.81
Adapting Genotyping-by-Sequencing for Rice F2 Populations. G3 (Bethesda) (2017) 0.81
Assessment of drought tolerance of 49 switchgrass (Panicum virgatum) genotypes using physiological and morphological parameters. Biotechnol Biofuels (2015) 0.81
GBS-SNP-CROP: a reference-optional pipeline for SNP discovery and plant germplasm characterization using variable length, paired-end genotyping-by-sequencing data. BMC Bioinformatics (2016) 0.80
Validation of Genotyping-By-Sequencing Analysis in Populations of Tetraploid Alfalfa by 454 Sequencing. PLoS One (2015) 0.79
Similarity thresholds used in DNA sequence assembly from short reads can reduce the comparability of population histories across species. PeerJ (2015) 0.79
Evolution of Gene Duplication in Plants. Plant Physiol (2016) 0.78
Sequencing-based high throughput mutation detection in bread wheat. BMC Genomics (2015) 0.78
Bioinformatic analysis of genotype by sequencing (GBS) data with NGSEP. BMC Genomics (2016) 0.78
Contrasting metabolism in perenniating structures of upland and lowland switchgrass plants late in the growing season. PLoS One (2014) 0.78
Genome-Wide Association Mapping and Genomic Selection for Alfalfa (Medicago sativa) Forage Quality Traits. PLoS One (2017) 0.78
Association analysis for disease resistance to Fusarium oxysporum in cape gooseberry (Physalis peruviana L). BMC Genomics (2016) 0.77
Neutral and Selective Processes Drive Population Differentiation for Iris hexagona. J Hered (2015) 0.77
Evaluation of Linkage Disequilibrium Pattern and Association Study on Seed Oil Content in Brassica napus Using ddRAD Sequencing. PLoS One (2016) 0.77
High-density marker profiling confirms ancestral genomes of Avena species and identifies D-genome chromosomes of hexaploid oat. Theor Appl Genet (2016) 0.77
Haplotag: Software for Haplotype-Based Genotyping-by-Sequencing Analysis. G3 (Bethesda) (2016) 0.77
A Parthenogenesis Gene Candidate and Evidence for Segmental Allopolyploidy in Apomictic Brachiaria decumbens. Genetics (2016) 0.76
Next-generation sampling: Pairing genomics with herbarium specimens provides species-level signal in Solidago (Asteraceae). Appl Plant Sci (2015) 0.76
Sequential Turnovers of Sex Chromosomes in African Clawed Frogs (Xenopus) Suggest Some Genomic Regions are Good at Sex Determination. G3 (Bethesda) (2016) 0.76
Exploiting genotyping by sequencing to characterize the genomic structure of the American cranberry through high-density linkage mapping. BMC Genomics (2016) 0.76
Population and Evolutionary Genomics of Amblyomma americanum, an Expanding Arthropod Disease Vector. Genome Biol Evol (2016) 0.76
TagDigger: user-friendly extraction of read counts from GBS and RAD-seq data. Source Code Biol Med (2016) 0.75
Population genomics of an endemic Mediterranean fish: differentiation by fine scale dispersal and adaptation. Sci Rep (2017) 0.75
Genotyping-by-Sequencing SNP Identification for Crops without a Reference Genome: Using Transcriptome Based Mapping as an Alternative Strategy. Front Plant Sci (2016) 0.75
Simple SNP-based minimal marker genotyping for Humulus lupulus L. identification and variety validation. BMC Res Notes (2015) 0.75
Genome-Wide Association Analysis of the Anthocyanin and Carotenoid Contents of Rose Petals. Front Plant Sci (2016) 0.75
Fast-GBS: a new pipeline for the efficient and highly accurate calling of SNPs from genotyping-by-sequencing data. BMC Bioinformatics (2017) 0.75
Discovery of Putative Herbicide Resistance Genes and Its Regulatory Network in Chickpea Using Transcriptome Sequencing. Front Plant Sci (2017) 0.75
Genetic Diversity, Population Structure, and Linkage Disequilibrium of a Core Collection of Ziziphus jujuba Assessed with Genome-wide SNPs Developed by Genotyping-by-sequencing and SSR Markers. Front Plant Sci (2017) 0.75
Genomic population structure of freshwater-resident and anadromous ide (Leuciscus idus) in north-western Europe. Ecol Evol (2016) 0.75
Lineage divergence, local adaptation across a biogeographic break, and artificial transport, shape the genetic structure in the ascidian Pyura chilensis. Sci Rep (2017) 0.75
Three Molecular Markers Show No Evidence of Population Genetic Structure in the Gouldian Finch (Erythrura gouldiae). PLoS One (2016) 0.75
Multiple Minor QTLs Are Responsible for Fusarium Head Blight Resistance in Chinese Wheat Landrace Haiyanzhong. PLoS One (2016) 0.75
Ecological genomics of local adaptation in Cornus florida L. by genotyping by sequencing. Ecol Evol (2016) 0.75
A genetic linkage map of black raspberry (Rubus occidentalis) and the mapping of Ag(4) conferring resistance to the aphid Amphorophora agathonica. Theor Appl Genet (2015) 0.75
The Genetic Basis of Upland/Lowland Ecotype Divergence in Switchgrass (Panicum virgatum). G3 (Bethesda) (2016) 0.75
QTL mapping and candidate genes for resistance to Fusarium ear rot and fumonisin contamination in maize. BMC Plant Biol (2017) 0.75
Transcriptome analysis in switchgrass discloses ecotype difference in photosynthetic efficiency. BMC Genomics (2016) 0.75
Genotype-by-sequencing facilitates genetic mapping of a stem rust resistance locus in Aegilops umbellulata, a wild relative of cultivated wheat. BMC Genomics (2016) 0.75
Using Genome-Wide SNP Discovery and Genotyping to Reveal the Main Source of Population Differentiation in Nothofagus dombeyi (Mirb.) Oerst. in Chile. Int J Genomics (2016) 0.75
Genotyping of whole genome amplified reduced representation libraries reveals a cryptic population of Culicoides brevitarsis in the Northern Territory, Australia. BMC Genomics (2016) 0.75
Improved tissue culture conditions for the emerging C4 model Panicum hallii. BMC Biotechnol (2017) 0.75
The report of my death was an exaggeration: A review for researchers using microsatellites in the 21st century. Appl Plant Sci (2016) 0.75
Inbreeding and selection shape genomic diversity in captive populations: Implications for the conservation of endangered species. PLoS One (2017) 0.75
Genetic Variation within Clonal Lineages of Phytophthora infestans Revealed through Genotyping-By-Sequencing, and Implications for Late Blight Epidemiology. PLoS One (2016) 0.75
The Impact of Genotyping-by-Sequencing Pipelines on SNP Discovery and Identification of Markers Associated with Verticillium Wilt Resistance in Autotetraploid Alfalfa (Medicago sativa L.). Front Plant Sci (2017) 0.75
Relative Performance of Non-Local Cultivars and Local, Wild Populations of Switchgrass (Panicum virgatum) in Competition Experiments. PLoS One (2016) 0.75
Large-scale SNP discovery and construction of a high-density genetic map of Colossoma macropomum through genotyping-by-sequencing. Sci Rep (2017) 0.75
Genome-Wide SNP Calling from Genotyping by Sequencing (GBS) Data: A Comparison of Seven Pipelines and Two Sequencing Technologies. PLoS One (2016) 0.75
A community resource for exploring and utilizing genetic diversity in the USDA pea single plant plus collection. Hortic Res (2017) 0.75
Genome-wide SNP identification, linkage map construction and QTL mapping for seed mineral concentrations and contents in pea (Pisum sativum L.). BMC Plant Biol (2017) 0.75
Genotyping-by-Sequencing in a Species Complex of Australian Hummock Grasses (Triodia): Methodological Insights and Phylogenetic Resolution. PLoS One (2017) 0.75
Genome-Wide Association Study Reveals Natural Variations Contributing to Drought Resistance in Crops. Front Plant Sci (2017) 0.75
Use of genotyping-by-sequencing to determine the genetic structure in the medicinal plant chamomile, and to identify flowering time and alpha-bisabolol associated SNP-loci by genome-wide association mapping. BMC Genomics (2017) 0.75
Genomic signatures of local adaptation reveal source-sink dynamics in a high gene flow fish species. Sci Rep (2017) 0.75
Mining sequence variations in representative polyploid sugarcane germplasm accessions. BMC Genomics (2017) 0.75
2b-RAD genotyping for population genomic studies of Chagas disease vectors: Rhodnius ecuadoriensis in Ecuador. PLoS Negl Trop Dis (2017) 0.75
Genotyping-by-Sequencing and Its Exploitation for Forage and Cool-Season Grain Legume Breeding. Front Plant Sci (2017) 0.75
Development of a high-density linkage map and mapping of the three-pistil gene (Pis1) in wheat using GBS markers. BMC Genomics (2017) 0.75
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The B73 maize genome: complexity, diversity, and dynamics. Science (2009) 18.73
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Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One (2008) 13.64
Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet (2011) 9.26
SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat Methods (2008) 8.26
Genetic properties of the maize nested association mapping population. Science (2009) 7.78
Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags. PLoS Genet (2010) 7.05
A first-generation haplotype map of maize. Science (2009) 6.82
Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc Natl Acad Sci U S A (2004) 6.66
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Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. PLoS One (2009) 5.26
Stacks: building and genotyping Loci de novo from short-read sequences. G3 (Bethesda) (2011) 4.99
Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content. PLoS Genet (2009) 3.88
Maize HapMap2 identifies extant variation from a genome in flux. Nat Genet (2012) 3.74
Multiplexed shotgun genotyping for rapid and efficient genetic mapping. Genome Res (2011) 3.63
Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley. BMC Genomics (2011) 3.42
High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. BMC Genomics (2010) 3.40
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Complete switchgrass genetic maps reveal subgenome collinearity, preferential pairing and multilocus interactions. Genetics (2010) 1.54
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Post-glacial evolution of Panicum virgatum: centers of diversity and gene pools revealed by SSR markers and cpDNA sequences. Genetica (2011) 1.21
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Comprehensive genotyping of the USA national maize inbred seed bank. Genome Biol (2013) 2.46
Population genomic and genome-wide association studies of agroclimatic traits in sorghum. Proc Natl Acad Sci U S A (2012) 2.40
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Dissection of maize kernel composition and starch production by candidate gene association. Plant Cell (2004) 2.27
Rare genetic variation at Zea mays crtRB1 increases beta-carotene in maize grain. Nat Genet (2010) 2.25
Genetic architecture of maize kernel composition in the nested association mapping and inbred association panels. Plant Physiol (2011) 2.20
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Distinct genetic architectures for male and female inflorescence traits of maize. PLoS Genet (2011) 1.88
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Aluminum tolerance in maize is associated with higher MATE1 gene copy number. Proc Natl Acad Sci U S A (2013) 1.63
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Population genetics of genomics-based crop improvement methods. Trends Genet (2011) 1.53
ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize. Proc Natl Acad Sci U S A (2012) 1.49
Heterosis is prevalent for multiple traits in diverse maize germplasm. PLoS One (2009) 1.45
The genetic architecture of maize height. Genetics (2014) 1.41
Joint QTL linkage mapping for multiple-cross mating design sharing one common parent. PLoS One (2011) 1.37
Lessons from Dwarf8 on the strengths and weaknesses of structured association mapping. PLoS Genet (2013) 1.30
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Genetic association mapping identifies single nucleotide polymorphisms in genes that affect abscisic acid levels in maize floral tissues during drought. J Exp Bot (2010) 1.27
Genic and nongenic contributions to natural variation of quantitative traits in maize. Genome Res (2012) 1.26
Can genomics boost productivity of orphan crops? Nat Biotechnol (2012) 1.24
Using natural allelic diversity to evaluate gene function. Methods Mol Biol (2003) 1.22
Post-glacial evolution of Panicum virgatum: centers of diversity and gene pools revealed by SSR markers and cpDNA sequences. Genetica (2011) 1.21
A modern ampelography: a genetic basis for leaf shape and venation patterning in grape. Plant Physiol (2013) 1.19
Genome-wide analysis of branched-chain amino acid levels in Arabidopsis seeds. Plant Cell (2013) 1.17
The genetic architecture of complex traits in teosinte (Zea mays ssp. parviglumis): new evidence from association mapping. Genetics (2008) 1.16
Elongated mesocotyl1, a phytochrome-deficient mutant of maize. Plant Physiol (2002) 1.13
Association and linkage analysis of aluminum tolerance genes in maize. PLoS One (2010) 1.12
Genome-wide association study and pathway-level analysis of tocochromanol levels in maize grain. G3 (Bethesda) (2013) 1.10
Natural variation in maize aphid resistance is associated with 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one glucoside methyltransferase activity. Plant Cell (2013) 1.10
Photomorphogenic responses in maize seedling development. Plant Physiol (2003) 1.07
Power to detect higher-order epistatic interactions in a metabolic pathway using a new mapping strategy. Genetics (2006) 1.07
Using crossover breakpoints in recombinant inbred lines to identify quantitative trait loci controlling the global recombination frequency. Genetics (2007) 1.05
The genetic architecture of maize stalk strength. PLoS One (2013) 1.03
Vitis phylogenomics: hybridization intensities from a SNP array outperform genotype calls. PLoS One (2013) 1.01
Software engineering the mixed model for genome-wide association studies on large samples. Brief Bioinform (2009) 1.00
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Subfunctionalization of PhyB1 and PhyB2 in the control of seedling and mature plant traits in maize. Plant J (2006) 0.98
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Genome size, quantitative genetics and the genomic basis for flower size evolution in Silene latifolia. Ann Bot (2005) 0.95
SNP discovery with EST and NextGen sequencing in switchgrass (Panicum virgatum L.). PLoS One (2012) 0.95
GDPC: connecting researchers with multiple integrated data sources. Bioinformatics (2004) 0.94
Panzea: an update on new content and features. Nucleic Acids Res (2007) 0.94
Optimizing on-farm pretreatment of perennial grasses for fuel ethanol production. Bioresour Technol (2010) 0.92
Genetic analysis of central carbon metabolism unveils an amino acid substitution that alters maize NAD-dependent isocitrate dehydrogenase activity. PLoS One (2010) 0.90
Dissecting genome-wide association signals for loss-of-function phenotypes in sorghum flavonoid pigmentation traits. G3 (Bethesda) (2013) 0.87
Natural variation in maize architecture is mediated by allelic differences at the PINOID co-ortholog barren inflorescence2. Plant J (2009) 0.86
Population genomic variation reveals roles of history, adaptation and ploidy in switchgrass. Mol Ecol (2014) 0.86
Species dependence of [64Cu]Cu-Bis(thiosemicarbazone) radiopharmaceutical binding to serum albumins. Nucl Med Biol (2008) 0.83
GAPIT Version 2: An Enhanced Integrated Tool for Genomic Association and Prediction. Plant Genome (2016) 0.82
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'Junk' DNA and phenotypic evolution in Silene section Siphonomorpha. Genet Res (Camb) (2008) 0.77
Nucleotide polymorphism and copy number variant detection using exome capture and next-generation sequencing in the polyploid grass Panicum virgatum. Plant J (2014) 0.77
Development of a High-Density Linkage Map and Tagging Leaf Spot Resistance in Pearl Millet Using Genotyping-by-Sequencing Markers. Plant Genome (2016) 0.76
Genome-Wide Association Study of Brown Stem Rot Resistance in Soybean across Multiple Populations. Plant Genome (2016) 0.76
Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation. Nat Genet (2017) 0.75
Has selection for improved agronomic traits made reed canarygrass invasive? PLoS One (2011) 0.75
Simple regression models as a threshold for selecting AFLP loci with reduced error rates. BMC Bioinformatics (2012) 0.75
CorrigendumMulti-Trait Genome-Wide Association Studies Reveal Loci Associated with Maize Inflorescence and Leaf Architecture. Plant Cell Physiol (2020) 0.75
Corrigendum: A study of allelic diversity underlying flowering-time adaptation in maize landraces. Nat Genet (2017) 0.75