Scientific Publications

Since 2007, the Floragenex team has proudly assisted scientists from around the world advance their research. Below you can find several examples of genomics work and a list of publications where Floragenex generated data or results for clients.


Featured Projects and Publications


Sequence-Based Genotyping for Marker Discovery and Co-Dominant Scoring in Germplasm and Populations

Researchers at KeyGene, N.V. describe the application of Sequence Based Genotyping (SBG) in Arabidopsis and Lactuca (lettuce) . In concert with the Illumina Genome Analyzer and HiSeq 2000 platforms, SBG was able to identify over 1,000 high quality genetic markers in each species, which were then used to assemble genetic linkage maps. The overall marker quality and dynamic range of marker density achievable with SBG is a valuable feature for assessing population structure or molecular assisted breeding applications.

 

Genome-wide association studies and prediction of 17 traits related to phenology, biomass and cell wall composition in the energy grass Miscanthus sinensis

Scientists at Aberystwyth University used RAD sequencing for a genome wide association study (GWAS) in the bioenergy feedstock Miscanthus. The goal in GWAS is to identify a set of genetic variants that tend to be associated with specific traits that are observed in natural, unstructured populations. RAD-Seq was able to identify over 100,000 single nucleotide variants (SNVs) across 138 Miscanthus plants. The large number of markers is advantageous in these types of studies, where understanding the organization of the genome at high resolution is key.


Rapid SNP Discovery and Genetic Mapping using Sequenced RAD markers

The pioneering paper describing the methods and protocols developed for Restriction-site Associated DNA Sequencing (RAD-Seq). As a proof of concept study, two populations of Danio rerio and Neurospora crassa were sequenced using the RAD method in conjunction with Illumina next generation DNA sequencing technology. Over 13,000 novel Single Nucleotide Polymorphisms (SNPs) were identified across both organisms. RAD-Seq also successfully identified several genetic loci known to regulate traits in both Danio and Neurospora, further demonstrating the applicability of the RAD platform for accurate genetic mapping. 

 

Client Institutions


Aarhus University
Aberystwyth University
BioDiagnostics
Duke University
Instituto Gulbenkian de Ciência
NCGR
New York University
North Dakota State University
Oregon State University
The Field Museum of Natural History   Trent University
The Morton Arboretum
Université Laval
University of Alberta
University of California - Berkeley
University of California - Irvine
University of California - Los Angeles
University of California - Santa Cruz
University of Fribourg
University of Georgia                       University of Idaho
University of Leuven                         University of Lyon
University of Minnesota
University of Oregon
University of Tennessee
University of Torino
USDA - Agricultural Research Service
Yale University

 

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Publications

  1. Genomic atolls of differentiation in coral reef fishes (Hypoplectrus spp., Serranidae). Puebla O, Bermingham E, McMillan WO. Mol Ecol. 2014 Nov;23(21):5291-303. doi: 10.1111/mec.12926. Epub 2014 Oct 4.
  2. A role for migration-linked genes and genomic islands in divergence of a songbird. Ruegg K, Anderson EC, Boone J, Pouls J, Smith TB. Mol Ecol. 2014 Oct;23(19):4757-69. doi: 10.1111/mec.12842. Epub 2014 Jul 8.
  3. Genotyping-by-sequencing as a tool to infer phylogeny and ancestral hybridization: A case study in Carex (Cyperaceae). Escudero M, Eaton DA, Hahn M, Hipp AL. Mol Phylogenet Evol. 2014 Oct;79:359-67. doi: 10.1016/j.ympev.2014.06.026. Epub 2014 Jul 8.
  4. Design of a 9K illumina BeadChip for polar bears (Ursus maritimus) from RAD and transcriptome sequencing. Malenfant RM, Coltman DW, Davis CS. Mol Ecol Resour. 2014 Sep 3. doi: 10.1111/1755-0998.12327. [Epub ahead of print]
  5. Genome-wide association studies and prediction of 17 traits related to phenology, biomass and cell wall composition in the energy grass Miscanthus sinensis. Slavov GT, Nipper R, Robson P, Farrar K, Allison GG, Bosch M, Clifton-Brown JC, Donnison IS, Jensen E. New Phytol. 2014 Mar;201(4):1227-39. doi: 10.1111/nph.12621. Epub 2013 Dec 6.
  6. Revisiting comparisons of genetic diversity in stable and declining species: assessing genome-wide polymorphism in North American bumble bees using RAD sequencing. Lozier JD. Mol Ecol. 2014 Feb;23(4):788-801. doi: 10.1111/mec.12636.
  7. Restriction site-associated DNA sequencing generates high-quality single nucleotide polymorphisms for assessing hybridization between bighead and silver carp in the United States and China. Lamer JT, Sass GG, Boone JQ, Arbieva ZH, Green SJ, Epifanio JM. Mol Ecol Resour. 2014 Jan;14(1):79-86. doi: 10.1111/1755-0998.12152. Epub 2013 Aug 20.
  8. A high-density SNP Map of sunflower derived from RAD-sequencing facilitating fine-mapping of the rust resistance gene R12. Talukder ZI, Gong L, Hulke BS, Pegadaraju V, Song Q, Schultz Q, Qi L. PLoS One. 2014;9(7):e98628. doi: 10.1371/journal.pone.0098628.
  9. A framework phylogeny of the American oak clade based on sequenced RAD data. Hipp AL, Eaton DA, Cavender-Bares J, Fitzek E, Nipper R, Manos PS. PLoS One. 2014;9(4):e93975. doi: 10.1371/journal.pone.0093975.
  10. The population genomics of repeated evolution in the blind cavefish Astyanax mexicanus. Bradic M, Teotonio H, Borowsky RL. Mol Biol Evol. 2013 Nov;30(11):2383-400. doi: 10.1093/molbev/mst136. Epub 2013 Aug 8.
  11. The genetic architecture of reproductive isolation during speciation-with-gene-flow in lake whitefish species pairs assessed by RAD sequencing. Gagnaire PA, Pavey SA, Normandeau E, Bernatchez L. Evolution. 2013 Sep;67(9):2483-97. doi: 10.1111/evo.12075. Epub 2013 Mar 9.
  12. Inferring phylogeny and introgression using RADseq data: an example from flowering plants (Pedicularis: Orobanchaceae). Eaton DA, Ree RH. Syst Biol. 2013 Sep;62(5):689-706. doi: 10.1093/sysbio/syt032. Epub 2013 May 7.
  13. De novo sequencing of sunflower genome for SNP discovery using RAD (Restriction site Associated DNA) approach. Pegadaraju V, Nipper R, Hulke B, Qi L, Schultz Q. BMC Genomics. 2013 Aug 15;14:556. doi: 10.1186/1471-2164-14-556.
  14. Mapping phenotypic, expression and transmission ratio distortion QTL using RAD markers in the Lake Whitefish (Coregonus clupeaformis). Gagnaire PA, Normandeau E, Pavey SA, Bernatchez L. Mol Ecol. 2013 Jun;22(11):3036-48. doi: 10.1111/mec.12127. Epub 2012 Nov 26.
  15. Genotyping by RAD sequencing enables mapping of fatty acid composition traits in perennial ryegrass (Lolium perenne (L.)). Hegarty M, Yadav R, Lee M, Armstead I, Sanderson R, Scollan N, Powell W, Skot L. Plant Biotechnol J. 2013 Jun;11(5):572-81. doi: 10.1111/pbi.12045. Epub 2013 Jan 18.
  16. SNP discovery using Paired-End RAD-tag sequencing on pooled genomic DNA of Sisymbrium austriacum (Brassicaceae). Vandepitte K, Honnay O, Mergeay J, Breyne P, Roldan-Ruiz I, De Meyer T. Mol Ecol Resour. 2013 Mar;13(2):269-75. doi: 10.1111/1755-0998.12039. Epub 2012 Dec 11.
  17. Genomic scan for single nucleotide polymorphisms reveals patterns of divergence and gene flow between ecologically divergent species. Stoelting KN, Nipper R, Lindtke D, Caseys C, Waeber S, Castiglione S, Lexer C. Mol Ecol. 2013 Feb;22(3):842-55. doi: 10.1111/mec.12011. Epub 2012 Sep 11.
  18. RAD tag sequencing as a source of SNP markers in Cynara cardunculus L. Scaglione D, Acquadro A, Portis E, Tirone M, Knapp SJ, Lanteri S. BMC Genomics. 2012 Jan 3;13:3. doi: 10.1186/1471-2164-13-3.
  19. A RAD tag derived marker based eggplant linkage map and the location of QTLs determining anthocyanin pigmentation. Barchi L, Lanteri S, Portis E, Vale G, Volante A, Pulcini L, Ciriaci T, Acciarri N, Barbierato V, Toppino L, Rotino GL. PLoS One. 2012;7(8):e43740. doi: 10.1371/journal.pone.0043740. Epub 2012 Aug 17.
  20. Identification of SNP and SSR markers in eggplant using RAD tag sequencing. Barchi L, Lanteri S, Portis E, Acquadro A, Vale G, Toppino L, Rotino GL. BMC Genomics. 2011 Jun 10;12:304. doi: 10.1186/1471-2164-12-304.
  21. Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne. Pfender WF, Saha MC, Johnson EA, Slabaugh MB. Theor Appl Genet. 2011 May;122(8):1467-80. doi: 10.1007/s00122-011-1546-3. Epub 2011 Feb 23.
  22. Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley. Chutimanitsakun Y, Nipper RW, Cuesta-Marcos A, Cistue L, Corey A, Filichkina T, Johnson EA, Hayes PM. BMC Genomics. 2011 Jan 4;12:4. doi: 10.1186/1471-2164-12-4.
  23. Rapid SNP discovery and genetic mapping using sequenced RAD markers. Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA. PLoS One. 2008;3(10):e3376. doi: 10.1371/journal.pone.0003376. Epub 2008 Oct 13.

Whitepaper Experimental Designs

Asanté™ Specimen and DNA Extraction Experimental Design

380 Sample High-Multiplex RAD-Seq Experimental Design