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

W-H Li, 1991, Low nucleotide diversity in man., Genetics, 129, 513, 10.1093/genetics/129.2.513

M Przeworski, 2000, Adjusting the focus on human variation., Trends Genet, 16, 296, 10.1016/S0168-9525(00)02030-8

Z Zhao, 2006, Nucleotide variation and haplotype diversity in a 10-kb noncoding region in three continental human populations., Genetics, 174, 399, 10.1534/genetics.106.060301

MI Tenaillon, 2001, Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp mays L.)., Proc Natl Acad Sci USA, 98, 9169, 10.1073/pnas.151244298

J Yan, 2009, Genetic characterization and linkage disequilibrium estimation of a global maize collection using SNP markers., PLoS One, 4, e8451, 10.1371/journal.pone.0008451

CF Aquadro, 2001, Genome-wide variation in human and fruitfly: a comparison., Curr Opin Genet Dev, 11, 627, 10.1016/S0959-437X(00)00245-8

SR Gill, 2005, Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant <italic>Staphylococcus aureus</italic> strain and a biofilm-producing methicillin-resistant <italic>Staphlococcus epidermis</italic> strain., J Bacteriol, 187, 2426, 10.1128/JB.187.7.2426-2438.2005

J Messing, 2006, Organization and variability of the maize genome., Curr Opin Plant Biol, 9, 157, 10.1016/j.pbi.2006.01.009

NM Springer, 2009, Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content., PLoS Genet, 5, e1000734, 10.1371/journal.pgen.1000734

J Lai, 2010, Genome-wide patterns of genetic variation among elite maize inbred lines., Nat Genet, 42, 1027, 10.1038/ng.684

ES Buckler, 2006, Molecular and functional diversity of maize., Curr Opin Plant Biol, 9, 172, 10.1016/j.pbi.2006.01.013

MA Gore, 2009, A first-generation haplotype map of maize., Science, 326, 1115, 10.1126/science.1177837

ML Metzker, 2010, Sequencing technologies – the next generation., Nat Rev Genet, 11, 31, 10.1038/nrg2626

DW Craig, 2008, Identification of genetic variants using bar-coded multiplexed sequencing., Nat Methods, 30, 887, 10.1038/nmeth.1251

R Cronn, 2008, Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology., Nucleic Acids Res, 36, e122, 10.1093/nar/gkn502

X Huang, 2009, High-throughput genotyping by whole-genome resequencing., Genome Res, 19, 1068, 10.1101/gr.089516.108

X Huang, 2010, Genome-wide association studies of 14 agronomic traits in rice landraces., Nat Genet, 42, 961, 10.1038/ng.695

L Mamanova, 2010, Target-enrichment strategies for next-generation sequencing., Nat Methods, 7, 111, 10.1038/nmeth.1419

M Gore, 2007, Evaluation of target preparation methods for single-feature polymorphism detection in large complex plant genomes., Crop Sci, 47, S135, 10.2135/cropsci2007.02.0085tpg

NA Baird, 2008, Rapid SNP discovery and genetic mapping using sequenced RAD markers., PLoS One, 3, e3376, 10.1371/journal.pone.0003376

PS Schnable, 2009, The B73 maize genome: complexity, diversity and dynamics., Science, 326, 1112, 10.1126/science.1178534

M Lee, 2002, Expanding the genetic map of maize with the intermated B73×Mo17 (IBM) population., Plant Mol Biol, 48, 453, 10.1023/A:1014893521186

JM Costa, 2001, Molecular mapping of the Oregon Wolfe Barleys: a phenotypically polymorphic doubled-haploid population., Theor Appl Genet, 103, 415, 10.1007/s001220100622

JJ Doyle, 1987, A rapid DNA isolation procedure for small quantities of fresh leaf tissue., Phytochem Bull, 19, 11

M Hamady, 2008, Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex., Nat Methods, 5, 235, 10.1038/nmeth.1184

DR Bentley, 2008, Accurate whole genome sequencing using reversible terminator chemistry., Nature, 456, 53, 10.1038/nature07517

H Li, 2009, Fast and accurate short read alignment with Burrows-Wheeler transform., Bioinformatics, 25, 1754, 10.1093/bioinformatics/btp324

SF Altschul, 1997, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs., Nucleic Acids Res, 25, 3389, 10.1093/nar/25.17.3389

MD McMullen, 2009, Genetic properties of the maize nested association mapping population., Science, 325, 737, 10.1126/science.1174320

DL Remington, 2001, Structure of linkage disequilibrium and phenotypic associations in the maize genome., Proc Natl Acad Sci USA, 98, 11479, 10.1073/pnas.201394398

P Szucs, 2009, An integrated resource for barley linkage map and malting quality QTL alignment., Plant Genome, 2, 134, 10.3835/plantgenome2008.01.0005

P Andolfatto, 2011, Multiplexed shotgun genotyping for rapid and efficient genetic mapping., Genome Res, 21, 10.1101/gr.115402.110

P Vos, 1995, AFLP: a new technique for DNA fingerprinting., Nucleic Acids Res, 23, 4407, 10.1093/nar/23.21.4407

M Fedurco, 2006, BTA, a novel reagent for DNA attachment on glass and efficient generation of solid–phase amplified DNA colonies., Nucleic Acids Res, 34, e22, 10.1093/nar/gnj023

S Salvi, 2007, Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize., Proc Natl Acad Sci USA, 104, 11376, 10.1073/pnas.0704145104

RM Clark, 2006, A distant upstream enhancer at the maize domestication gene <italic>tb1</italic> has pleiotropic effects on plant and inflorescent architecture., Nature Genet, 38, 594, 10.1038/ng1784

MA Arteaga-Vazquez, 2010, Paramutation in maize: RNA mediated <italic>trans</italic>-generational gene silencing., Curr Opin Genet Dev, 20, 156, 10.1016/j.gde.2010.01.008