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Validation of Genotyping by Sequencing Using Transcriptomics for Diversity and Application of Genomic Selection in Tetraploid Potato.

Caruana BM, Pembleton LW, Constable F, Rodoni B, Slater AT, Cogan NOI.

Front Plant Sci. 2019 May 29;10:670. doi: 10.3389/fpls.2019.00670. eCollection 2019.


Development and Application of Droplet Digital PCR Tools for the Detection of Transgenes in Pastures and Pasture-Based Products.

Giraldo PA, Cogan NOI, Spangenberg GC, Smith KF, Shinozuka H.

Front Plant Sci. 2019 Jan 8;9:1923. doi: 10.3389/fpls.2018.01923. eCollection 2018.


Evaluation and Recommendations for Routine Genotyping Using Skim Whole Genome Re-sequencing in Canola.

Malmberg MM, Barbulescu DM, Drayton MC, Shinozuka M, Thakur P, Ogaji YO, Spangenberg GC, Daetwyler HD, Cogan NOI.

Front Plant Sci. 2018 Dec 7;9:1809. doi: 10.3389/fpls.2018.01809. eCollection 2018.


Evaluation of endophyte toxin production and its interaction with transgenic perennial ryegrass (Lolium perenne L.) with altered expression of fructosyltransferases.

Giraldo PA, Elliott C, Badenhorst P, Kearney G, Spangenberg GC, Cogan NOI, Smith KF.

Transgenic Res. 2018 Oct;27(5):397-407. doi: 10.1007/s11248-018-0087-9. Epub 2018 Jul 20.


Genomic Prediction Using Prior Quantitative Trait Loci Information Reveals a Large Reservoir of Underutilised Blackleg Resistance in Diverse Canola (Brassica napus L.) Lines.

Fikere M, Barbulescu DM, Malmberg MM, Shi F, Koh JCO, Slater AT, MacLeod IM, Bowman PJ, Salisbury PA, Spangenberg GC, Cogan NOI, Daetwyler HD.

Plant Genome. 2018 Jul;11(2). doi: 10.3835/plantgenome2017.11.0100.


Exploitation of data from breeding programs supports rapid implementation of genomic selection for key agronomic traits in perennial ryegrass.

Pembleton LW, Inch C, Baillie RC, Drayton MC, Thakur P, Ogaji YO, Spangenberg GC, Forster JW, Daetwyler HD, Cogan NOI.

Theor Appl Genet. 2018 Sep;131(9):1891-1902. doi: 10.1007/s00122-018-3121-7. Epub 2018 Jun 2.


Diversity and Genome Analysis of Australian and Global Oilseed Brassica napus L. Germplasm Using Transcriptomics and Whole Genome Re-sequencing.

Malmberg MM, Shi F, Spangenberg GC, Daetwyler HD, Cogan NOI.

Front Plant Sci. 2018 Apr 19;9:508. doi: 10.3389/fpls.2018.00508. eCollection 2018.


Genotyping-by-sequencing through transcriptomics: implementation in a range of crop species with varying reproductive habits and ploidy levels.

Malmberg MM, Pembleton LW, Baillie RC, Drayton MC, Sudheesh S, Kaur S, Shinozuka H, Verma P, Spangenberg GC, Daetwyler HD, Forster JW, Cogan NOI.

Plant Biotechnol J. 2018 Apr;16(4):877-889. doi: 10.1111/pbi.12835. Epub 2017 Oct 13.


Metagenomic arbovirus detection using MinION nanopore sequencing.

Batovska J, Lynch SE, Rodoni BC, Sawbridge TI, Cogan NO.

J Virol Methods. 2017 Nov;249:79-84. doi: 10.1016/j.jviromet.2017.08.019. Epub 2017 Sep 4.


Reference transcriptome assembly and annotation for perennial ryegrass.

Shinozuka H, Cogan NOI, Spangenberg GC, Forster JW.

Genome. 2017 Dec;60(12):1086-1088. doi: 10.1139/gen-2017-0077. Epub 2017 Aug 25.


Horizontal transfer of a ß-1,6-glucanase gene from an ancestral species of fungal endophyte to a cool-season grass host.

Shinozuka H, Hettiarachchige IK, Shinozuka M, Cogan NOI, Spangenberg GC, Cocks BG, Forster JW, Sawbridge TI.

Sci Rep. 2017 Aug 22;7(1):9024. doi: 10.1038/s41598-017-07886-2.


Effective mosquito and arbovirus surveillance using metabarcoding.

Batovska J, Lynch SE, Cogan NOI, Brown K, Darbro JM, Kho EA, Blacket MJ.

Mol Ecol Resour. 2018 Jan;18(1):32-40. doi: 10.1111/1755-0998.12682. Epub 2017 May 15.


Improving Genetic Gain with Genomic Selection in Autotetraploid Potato.

Slater AT, Cogan NO, Forster JW, Hayes BJ, Daetwyler HD.

Plant Genome. 2016 Nov;9(3). doi: 10.3835/plantgenome2016.02.0021. Review.


Genetic Gain and Inbreeding from Genomic Selection in a Simulated Commercial Breeding Program for Perennial Ryegrass.

Lin Z, Cogan NO, Pembleton LW, Spangenberg GC, Forster JW, Hayes BJ, Daetwyler HD.

Plant Genome. 2016 Mar;9(1). doi: 10.3835/plantgenome2015.06.0046.


SNP-Based Linkage Mapping for Validation of QTLs for Resistance to Ascochyta Blight in Lentil.

Sudheesh S, Rodda MS, Davidson J, Javid M, Stephens A, Slater AT, Cogan NO, Forster JW, Kaur S.

Front Plant Sci. 2016 Nov 2;7:1604. eCollection 2016.


Generation and Characterisation of a Reference Transcriptome for Lentil (Lens culinaris Medik.).

Sudheesh S, Verma P, Forster JW, Cogan NO, Kaur S.

Int J Mol Sci. 2016 Nov 12;17(11). pii: E1887.


Using Next-Generation Sequencing for DNA Barcoding: Capturing Allelic Variation in ITS2.

Batovska J, Cogan NO, Lynch SE, Blacket MJ.

G3 (Bethesda). 2017 Jan 5;7(1):19-29. doi: 10.1534/g3.116.036145.


Targeted genotyping-by-sequencing permits cost-effective identification and discrimination of pasture grass species and cultivars.

Pembleton LW, Drayton MC, Bain M, Baillie RC, Inch C, Spangenberg GC, Wang J, Forster JW, Cogan NO.

Theor Appl Genet. 2016 May;129(5):991-1005. doi: 10.1007/s00122-016-2678-2. Epub 2016 Feb 16.


Validation of molecular markers associated with boron tolerance, powdery mildew resistance and salinity tolerance in field peas.

Javid M, Rosewarne GM, Sudheesh S, Kant P, Leonforte A, Lombardi M, Kennedy PR, Cogan NO, Slater AT, Kaur S.

Front Plant Sci. 2015 Oct 27;6:917. doi: 10.3389/fpls.2015.00917. eCollection 2015.


Design of an F1 hybrid breeding strategy for ryegrasses based on selection of self-incompatibility locus-specific alleles.

Pembleton LW, Shinozuka H, Wang J, Spangenberg GC, Forster JW, Cogan NO.

Front Plant Sci. 2015 Sep 24;6:764. doi: 10.3389/fpls.2015.00764. eCollection 2015.


De novo assembly and characterisation of the field pea transcriptome using RNA-Seq.

Sudheesh S, Sawbridge TI, Cogan NO, Kennedy P, Forster JW, Kaur S.

BMC Genomics. 2015 Aug 16;16:611. doi: 10.1186/s12864-015-1815-7.


A simple method for semi-random DNA amplicon fragmentation using the methylation-dependent restriction enzyme MspJI.

Shinozuka H, Cogan NO, Shinozuka M, Marshall A, Kay P, Lin YH, Spangenberg GC, Forster JW.

BMC Biotechnol. 2015 Apr 11;15:25. doi: 10.1186/s12896-015-0139-7.


Assessment of genetic variation within a global collection of lentil (Lens culinaris Medik.) cultivars and landraces using SNP markers.

Lombardi M, Materne M, Cogan NO, Rodda M, Daetwyler HD, Slater AT, Forster JW, Kaur S.

BMC Genet. 2014 Dec 24;15:150. doi: 10.1186/s12863-014-0150-3.


Improving breeding efficiency in potato using molecular and quantitative genetics.

Slater AT, Cogan NO, Hayes BJ, Schultz L, Dale MF, Bryan GJ, Forster JW.

Theor Appl Genet. 2014 Nov;127(11):2279-92. doi: 10.1007/s00122-014-2386-8. Epub 2014 Sep 4. Review.


Gene discovery and molecular marker development, based on high-throughput transcript sequencing of Paspalum dilatatum Poir.

Giordano A, Cogan NO, Kaur S, Drayton M, Mouradov A, Panter S, Schrauf GE, Mason JG, Spangenberg GC.

PLoS One. 2014 Feb 10;9(2):e85050. doi: 10.1371/journal.pone.0085050. eCollection 2014.


SNP discovery and high-density genetic mapping in faba bean (Vicia faba L.) permits identification of QTLs for ascochyta blight resistance.

Kaur S, Kimber RB, Cogan NO, Materne M, Forster JW, Paull JG.

Plant Sci. 2014 Mar;217-218:47-55. doi: 10.1016/j.plantsci.2013.11.014. Epub 2013 Dec 1.


Improving the analysis of low heritability complex traits for enhanced genetic gain in potato.

Slater AT, Wilson GM, Cogan NO, Forster JW, Hayes BJ.

Theor Appl Genet. 2014 Apr;127(4):809-20. doi: 10.1007/s00122-013-2258-7. Epub 2013 Dec 29.


EST-SNP discovery and dense genetic mapping in lentil (Lens culinaris Medik.) enable candidate gene selection for boron tolerance.

Kaur S, Cogan NO, Stephens A, Noy D, Butsch M, Forster JW, Materne M.

Theor Appl Genet. 2014 Mar;127(3):703-13. doi: 10.1007/s00122-013-2252-0. Epub 2013 Dec 27.


Nucleotide diversity of vernalization and flowering-time-related genes in a germplasm collection of meadow fescue (Festuca pratensis Huds. syn. Lolium pratense (Huds.) Darbysh.).

Shinozuka H, Hand ML, Cogan NO, Spangenberg GC, Forster JW.

Ecol Evol. 2013 Nov;3(13):4415-26. doi: 10.1002/ece3.828. Epub 2013 Oct 9.


SNP marker discovery, linkage map construction and identification of QTLs for enhanced salinity tolerance in field pea (Pisum sativum L.).

Leonforte A, Sudheesh S, Cogan NO, Salisbury PA, Nicolas ME, Materne M, Forster JW, Kaur S.

BMC Plant Biol. 2013 Oct 17;13:161. doi: 10.1186/1471-2229-13-161.


StAMPP: an R package for calculation of genetic differentiation and structure of mixed-ploidy level populations.

Pembleton LW, Cogan NO, Forster JW.

Mol Ecol Resour. 2013 Sep;13(5):946-52. doi: 10.1111/1755-0998.12129. Epub 2013 Jun 6.


Plastome Sequence Determination and Comparative Analysis for Members of the Lolium-Festuca Grass Species Complex.

Hand ML, Spangenberg GC, Forster JW, Cogan NO.

G3 (Bethesda). 2013 Apr 9;3(4):607-616. doi: 10.1534/g3.112.005264.


Quantitative Trait Locus (QTL) meta-analysis and comparative genomics for candidate gene prediction in perennial ryegrass (Lolium perenne L.).

Shinozuka H, Cogan NO, Spangenberg GC, Forster JW.

BMC Genet. 2012 Nov 8;13:101. doi: 10.1186/1471-2156-13-101.


Transcriptome sequencing of field pea and faba bean for discovery and validation of SSR genetic markers.

Kaur S, Pembleton LW, Cogan NO, Savin KW, Leonforte T, Paull J, Materne M, Forster JW.

BMC Genomics. 2012 Mar 20;13:104. doi: 10.1186/1471-2164-13-104.


Comparative Genomics in Perennial Ryegrass (Lolium perenne L.): Identification and Characterisation of an Orthologue for the Rice Plant Architecture-Controlling Gene OsABCG5.

Shinozuka H, Cogan NO, Spangenberg GC, Forster JW.

Int J Plant Genomics. 2011;2011:291563. doi: 10.1155/2011/291563. Epub 2011 Sep 15.


Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery.

Kaur S, Cogan NO, Pembleton LW, Shinozuka M, Savin KW, Materne M, Forster JW.

BMC Genomics. 2011 May 25;12:265. doi: 10.1186/1471-2164-12-265.


Development and validation of a TaqMan PCR assay for the Australian abalone herpes-like virus.

Corbeil S, Colling A, Williams LM, Wong FY, Savin K, Warner S, Murdoch B, Cogan NO, Sawbridge TI, Fegan M, Mohammad I, Sunarto A, Handlinger J, Pyecroft S, Douglas M, Changs PH, Crane MS.

Dis Aquat Organ. 2010 Oct 26;92(1):1-10. doi: 10.3354/dao02277.


Identification of QTLs for morphological traits influencing waterlogging tolerance in perennial ryegrass (Lolium perenne L.).

Pearson A, Cogan NO, Baillie RC, Hand ML, Bandaranayake CK, Erb S, Wang J, Kearney GA, Gendall AR, Smith KF, Forster JW.

Theor Appl Genet. 2011 Feb;122(3):609-22. doi: 10.1007/s00122-010-1473-8. Epub 2010 Oct 28.


Evolutionary history of tall fescue morphotypes inferred from molecular phylogenetics of the Lolium-Festuca species complex.

Hand ML, Cogan NO, Stewart AV, Forster JW.

BMC Evol Biol. 2010 Oct 12;10:303. doi: 10.1186/1471-2148-10-303.


Comparison of homoeolocus organisation in paired BAC clones from white clover (Trifolium repens L.) and microcolinearity with model legume species.

Hand ML, Cogan NO, Sawbridge TI, Spangenberg GC, Forster JW.

BMC Plant Biol. 2010 May 24;10:94. doi: 10.1186/1471-2229-10-94.


Fine-scale comparative genetic and physical mapping supports map-based cloning strategies for the self-incompatibility loci of perennial ryegrass (Lolium perenne L.).

Shinozuka H, Cogan NO, Smith KF, Spangenberg GC, Forster JW.

Plant Mol Biol. 2010 Feb;72(3):343-55. doi: 10.1007/s11103-009-9574-y. Epub 2009 Nov 27.


Identification of genetic factors influencing salt stress tolerance in white clover (Trifolium repens L.) by QTL analysis.

Wang J, Drayton MC, George J, Cogan NO, Baillie RC, Hand ML, Kearney GA, Erb S, Wilkinson T, Bannan NR, Forster JW, Smith KF.

Theor Appl Genet. 2010 Feb;120(3):607-19. doi: 10.1007/s00122-009-1179-y. Epub 2009 Oct 29.


Genetic map construction and QTL mapping of resistance to blackleg (Leptosphaeria maculans) disease in Australian canola (Brassica napus L.) cultivars.

Kaur S, Cogan NO, Ye G, Baillie RC, Hand ML, Ling AE, McGearey AK, Kaur J, Hopkins CJ, Todorovic M, Mountford H, Edwards D, Batley J, Burton W, Salisbury P, Gororo N, Marcroft S, Kearney G, Smith KF, Forster JW, Spangenberg GC.

Theor Appl Genet. 2009 Dec;120(1):71-83. doi: 10.1007/s00122-009-1160-9. Epub 2009 Oct 11.


Molecular characterisation and genetic mapping of candidate genes for qualitative disease resistance in perennial ryegrass (Lolium perenne L.).

Dracatos PM, Cogan NO, Sawbridge TI, Gendall AR, Smith KF, Spangenberg GC, Forster JW.

BMC Plant Biol. 2009 May 19;9:62. doi: 10.1186/1471-2229-9-62.


Comparison of genome structure between white clover and Medicago truncatula supports homoeologous group nomenclature based on conserved synteny.

George J, Sawbridge TI, Cogan NO, Gendall AR, Smith KF, Spangenberg GC, Forster JW.

Genome. 2008 Nov;51(11):905-11. doi: 10.1139/G08-076.


Identification of homologous, homoeologous and paralogous sequence variants in an outbreeding allopolyploid species based on comparison with progenitor taxa.

Hand ML, Ponting RC, Drayton MC, Lawless KA, Cogan NO, Charles Brummer E, Sawbridge TI, Spangenberg GC, Smith KF, Forster JW.

Mol Genet Genomics. 2008 Oct;280(4):293-304. doi: 10.1007/s00438-008-0365-y. Epub 2008 Jul 19.


Discovery and genetic mapping of single nucleotide polymorphisms in candidate genes for pathogen defence response in perennial ryegrass (Lolium perenne L.).

Dracatos PM, Cogan NO, Dobrowolski MP, Sawbridge TI, Spangenberg GC, Smith KF, Forster JW.

Theor Appl Genet. 2008 Jul;117(2):203-19. doi: 10.1007/s00122-008-0766-7. Epub 2008 May 1.


SNP discovery, validation, haplotype structure and linkage disequilibrium in full-length herbage nutritive quality genes of perennial ryegrass (Lolium perenne L.).

Ponting RC, Drayton MC, Cogan NO, Dobrowolski MP, Spangenberg GC, Smith KF, Forster JW.

Mol Genet Genomics. 2007 Nov;278(5):585-97. Epub 2007 Jul 24.


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