Genotyping by sequencing references

advertisement
Genotyping by Sequencing references
Amish S.J., Hohenlohe P.A., Painter S. et al. (2012) RAD sequencing yields a high success rate for
westslope cutthroat and rainbow trout species-diagnostic SNP assays. Molecular Ecology Resources 12,
653-660.
Amores A., Catchen J., Ferrara A., Fontenot Q., Postlethwait J.H. (2011) Genome Evolution and Meiotic
Maps by Massively Parallel DNA Sequencing: Spotted Gar, an Outgroup for the Teleost Genome
Duplication. Genetics 188, 799-U779.
Baird N.A., Etter P.D., Atwood T.S. et al. (2008) Rapid SNP Discovery and Genetic Mapping Using
Sequenced RAD Markers. PLoS ONE 3.
Barchi L., Lanteri S., Portis E. et al. (2011) Identification of SNP and SSR markers in eggplant using RAD
tag sequencing. Bmc Genomics 12.
Baxter S.W., Davey J.W., Johnston J.S. et al. (2011) Linkage mapping and comparative genomics using
next-generation RAD gequencing of a non-model organism. Plos One 6.
Chutimanitsakun Y., Nipper R.W., Cuesta-Marcos A. et al. (2011) Construction and application for QTL
analysis of a Restriction Site Associated DNA (RAD) linkage map in barley. Bmc Genomics 12.
Crouch J., Oudemans P., Polashock J. (2010) Sequenced restriction-associated DNA (RAD) markers for
SNP discovery in the genus Colletotrichum. Phytopathology 100, S27-S27.
Davey J.W., Blaxter M.L. (2011) RADSeq: next-generation population genetics (vol 9, pg 416, 2010).
Briefings in Functional Genomics 10, 108-108.
Davey J.W., Hohenlohe P.A., Etter P.D., Boone J.Q., Catchen J.M., Blaxter M.L. (2011) Genome-wide
genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 12, 499-510.
Elshire R.J., Glaubitz J.C., Sun Q. et al. (2011) A Robust, Simple Genotyping-by-Sequencing (GBS)
Approach for High Diversity Species. PLoS ONE 6.
Emerson K.J., Merz C.R., Catchen J.M. et al. (2010) Resolving postglacial phylogeography using highthroughput sequencing. Proceedings of the National Academy of Sciences of the United States of
America 107, 16196-16200.
Etter P.D., Preston J.L., Bassham S., Cresko W.A., Johnson E.A. (2011) Local De Novo Assembly of RAD
Paired-End Contigs Using Short Sequencing Reads. Plos One 6.
Hohenlohe P.A., Amish S.J., Catchen J.M., Allendorf F.W., Luikart G. (2011) Next-generation RAD
sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope
cutthroat trout. Molecular Ecology Resources 11, 117-122.
Hohenlohe P.A., Bassham S., Currey M., Cresko W.A. (2012) Extensive linkage disequilibrium and parallel
adaptive divergence across threespine stickleback genomes. Philosophical Transactions of the Royal
Society B-Biological Sciences 367, 395-408.
Hohenlohe P.A., Bassham S., Etter P.D., Stiffler N., Johnson E.A., Cresko W.A. (2010) Population
genomics of parallel adaptation in threespine stickleback using sequenced RAD Tags. PLOS Genetics 6.
Houston R.D., Davey J.L., Bishop S.C. et al. (2012) Characterisation of QTL-linked and genome-wide
restriction site-associated DNA (RAD) markers in farmed Atlantic salmon. BMC Genomics 13, 244.
McCormack J.E., Maley J.M., Hird S.M., Derryberry E.P., Graves G.R., Brumfield R.T. (2012) Nextgeneration sequencing reveals phylogeographic structure and a species tree for recent bird divergences.
Molecular Phylogenetics and Evolution 62, 397-406.
Miller M.R., Brunelli J.P., Wheeler P.A. et al. (2012) A conserved haplotype controls parallel adaptation
in geographically distant salmonid populations. Molecular Ecology 21, 237-249.
Nadeau N.J., Whibley A., Jones R.T. et al. (2012) Genomic islands of divergence in hybridizing Heliconius
butterflies identified by large-scale targeted sequencing. Philosophical Transactions of the Royal Society
B-Biological Sciences 367, 343-353.
O'Rourke S.M., Yochem J., Connolly A.A. et al. (2011) Rapid Mapping and Identification of Mutations in
Caenorhabditis elegans by Restriction Site-Associated DNA Mapping and Genomic Interval Pull-Down
Sequencing. Genetics 189, 767-U108.
Pfender W.F., Saha M.C., Johnson E.A., Slabaugh M.B. (2011) Mapping with RAD (restriction-site
associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne. Theoretical
and Applied Genetics 122, 1467-1480.
Poland J.A., Brown P.J., Sorrells M.E., Jannink J.L. (2012) Development of High-Density Genetic Maps for
Barley and Wheat Using a Novel Two-Enzyme Genotyping-by-Sequencing Approach. PLoS ONE 7.
Puritz J.B., Addison J.A., Toonen R.J. (2012) Next-Generation Phylogeography: A Targeted Approach for
Multilocus Sequencing of Non-Model Organisms. PLoS ONE 7.
Scaglione D., Acquadro A., Portis E., Tirone M., Knapp S.J., Lanteri S. (2012) RAD tag sequencing as a
source of SNP markers in Cynara cardunculus L. Bmc Genomics 13.
Twyford A.D., Ennos R.A. (2012) Next-generation hybridization and introgression. Heredity 108, 179-189.
Willing E.M., Hoffmann M., Klein J.D., Weigel D., Dreyer C. (2011) Paired-end RAD-seq for de novo
assembly and marker design without available reference. Bioinformatics 27, 2187-2193.
Download