Publications DE

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Publications - David Edwards

BOOKS:

  1. Plant Genomics and Climate Change. Eds. Edwards D. and Batley J. Springer (USA). (2015) (in press)
  2. Plant Bioinformatics (Second Edition). Ed. Edwards D. Methods in Molecular Biology, Springer (USA). (2015) (in press)
  3. Genetics, Genomics and Breeding of Oilseed Brassicas. Edwards D, Parkin IAP and Batley J. Science Publishers, (USA). (2012)
  4. Bioinformatics: Tools and Applications. Ed. Edwards D, Hanson D and Stajich J. Springer (USA). (2009)
  5. Plant Bioinformatics. Ed. Edwards D. Methods in Molecular Biology, Humana Press (USA). (2007)

BOOK CHAPTERS:

  1. Edwards D. (2015) The impact of genomics technology on adapting plants to climate change. In: Plant Genomics and Climate Change. Eds. Edwards D. and Batley J. Springer (USA), (in press)
  2. Ruperao P and Edwards D. (2015) Bioinformatics: Identification of markers from next-generation sequence data. In: Plant Genotyping. Ed. Batley J. Methods in Molecular Biology, Springer (USA), pp. 29-47
  3. Lai K, Lorenc MT and Edwards D. (2015) Molecular marker databases. In: Plant Genotyping. Ed. Batley J. Methods in Molecular Biology, Springer (USA), pp. 49-62
  4. Golicz AA, Bayer PE and Edwards D. (2015) Skim-based genotyping by sequencing. In: Plant Genotyping. Ed. Batley J. Methods in Molecular Biology, Springer (USA), pp. 257-270
  5. Visendi P, Batley J and Edwards D. Next Generation Sequencing and Germplasm Resources. In Advances in Genomics of Plant Genetic resources. Volume 1. Genomics platforms, crop domestication and allele mining. Ed. Tuberosa R. Springer (USA) (accepted August 2012)
  6. Edwards D. (2013) Bioinformatics tools to assist breeding for climate change. In Genomics and breeding for climate resilient crops. Ed, Kole C. Springer (USA), pp 391-414
  7. Edwards D and Gupta PK. (2013) Sequence based DNA markers and genotyping for cereal genomics and breeding. In Cereal Genomics II. Eds. Gupta PK and Varshney, RK. Springer (USA) pp 57-76
  8. Edwards D and Wang X. (2012) Genome Sequencing Initiatives. In Genetics, Genomics and Breeding of Oilseed Brassicas. Edwards D, Parkin IAP and Batley J. Science Publishers, (USA) pp 152-157
  9. Lorenc M, Boskovic Z, Stiller J, Duran C and Edwards D. (2012) Role of Bioinformatics as a Tool for Oilseed Brassica Species. In Genetics, Genomics and Breeding of Oilseed Brassicas. Edwards D, Parkin IAP and Batley J. Science Publishers, (USA) pp 194-205
  10. Edwards D. (2011) Wheat Bioinformatics. In: The World Wheat Book II. Eds. Bonjean A, Angus W and Van Ginkel M. Lavoisier (France) pp 851-875
  11. Duran C, Boskovic Z, Batley J and Edwards D. (2011) Brassica Bioinformatics. In Vegetable Brassicas Ed. Sadowski J. Science Publishers, Inc., New Hampshire pp 406-418
  12. Edwards D, Hansen D and Stajich J. (2009) DNA Sequence Databases. In Bioinformatics: Tools and Applications. Ed. Edwards D, Hanson D and Stajich J. Springer (USA), pp 1-11
  13. Duran C, Edwards D and Batley J. (2009) Molecular Marker Discovery and Genetic map Visualisation. In Bioinformatics: Tools and Applications. Ed. Edwards D, Hanson D and Stajich J. Springer (USA), pp 165-189
  14. Imelfort M, Batley J, Grimmond S and Edwards D. (2009) Genome sequencing approaches and successes. In: Plant Genomics. Ed. Somers D, Langridge P, and Gustafson JP. Methods in Molecular Biology, Humana Press (USA), pp 345-358
  15. Batley J and Edwards D. (2009) Mining for Single Nucleotide Polymorphism (SNP) and Simple Sequence Repeat (SSR) molecular genetic markers. In: Bioinformatics for DNA Sequence Analysis. Ed. Posada D. Methods in Molecular Biology, Humana Press (USA), pp 303-322
  16. Appleby N, Edwards D and Batley J. (2009) New technologies for ultra-high throughput genotyping in plants. In: Plant Genomics. Ed. Somers D, Langridge P, and Gustafson JP. Methods in Molecular Biology, Humana Press, (USA), pp 19-40
  17. Duran C, Edwards D and Batley J. (2009) Genetic maps and the use of synteny. In: Plant Genomics. Ed. Somers D, Langridge P, and Gustafson JP. Methods in Molecular Biology, Humana Press (USA), pp 41-56
  18. Edwards D and Batley J. (2008) Bioinformatics: Fundamentals and Applications in Plant Genetics, Mapping and Breeding. In: Principles and Practices of Plant Genomics. Eds. Kole C and Abbott AG. Science Publishers, Inc., (USA), pp 269-302
  19. Edwards D. (2007) Bioinformatics and plant genomics for staple crops improvement. In: Breeding Major Food Staples. Eds. Kang MS and Priyadarshan PM. Blackwell, pp 93-106
  20. Batley J, Jewell E and Edwards D. (2007) Automated discovery of Single Nucleotide Polymorphism (SNP) and Simple Sequence Repeat (SSR) molecular genetic markers. In: Plant Bioinformatics. Ed. Edwards D. Methods in Molecular Biology, Humana Press (USA), pp. 473-494
  21. Love CG and Edwards D. (2007) Accessing integrated Brassica genetic and genomic data using the BASC server. In: Plant Bioinformatics. Ed. Edwards D. Methods in Molecular Biology, Humana Press (USA) (2007), pp. 229-244
  22. Edwards D, Salisbury PA, Burton WA, Hopkins CJ and Batley J. (2007) Indian Mustard, in Genome Mapping and Molecular Breeding in Plants, Vol. 2. Ed. Kole C. Springer NY, pp 179-210
  23. Edwards D, Forster JW, Chagné D and Batley J. (2007) What are SNPs? In: Association Mapping in Plants Eds. Oraguzie NC, Rikkerink EHA, Gardiner SE and De Silva HN. Springer NY, pp 41-52.
  24. Edwards D, Batley J, Cogan NOI, Forster JW and Chagné D. 2007. Single Nucleotide Polymorphism Discovery. In: Association Mapping in Plants Eds. Oraguzie NC, Rikkerink EHA, Gardiner SE and De Silva HN. Springer NY, pp 53-76.
  25. Chagné D, Batley J, Edwards D, and Forster JW. (2007) Single Nucleotide Polymorphisms genotyping in plants. In: Association Mapping in Plants Eds. Oraguzie NC, Rikkerink EHA, Gardiner SE and De Silva HN. Springer NY, pp 77-94.
  26. Batley J and Edwards D. (2007) SNP applications in plants. In: Association Mapping in Plants Eds. Oraguzie NC, Rikkerink EHA, Gardiner SE and De Silva HN. Springer NY, pp 95-102.
  27. Spangenberg GC, Forster JW, Edwards D, John U, Mouradov A, Emmerling M, Batley J, Felitti S, Cogan NOI, Smith KF and Dobrowolski M. (2005) Future Directions in the Molecular Breeding of Forage and Turf. In: Molecular Breeding for Genetic Improvement of Forage Crops and Turf. Ed. Humphreys MO. Wageningen Academic Publishers, pp 83-97.
  28. Spangenberg GC, Felitti SA, Shields K, Ramsperger M, Tian P, Ong EK, Singh D, Logan E and Edwards D. (2005) Gene Discovery and Microarray-Based Transcriptome Analysis of the Grass-Endophyte Association. In: Neotyphodium in Cool Season Grasses. Eds. Roberts CA, West CP and Spiers DE. Blackwell, pp 103-140

JOURNAL ARTICLES:

  1. Varshney RK, Singh VK, Xun X, Marshall DF, Wang J and Edwards D. (2015) Analytical and decision support tools for genomics-assisted breeding. Trends in Plant Science. (accepted October 2015)
  2. Golicz A, Batley J and Edwards D. (2015) Towards plant pangenomics. Plant Biotechnology Journal. (accepted October 2015)
  3. Kaniewska P, Chan CKK, Kline D, Ling EYS, Rosic N, Edwards D, Hoegh-Guldberg, Dove S. (2015) Transcriptomic changes in coral holobionts provide insights into physiological challenges of future climate and ocean change. PLOS ONE. (accepted September 2015)
  4. Kale SM, Jaganathan D, Ruperao P, Chen C, Punna R, Kudapa H, Thudi M, Roorkiwal M, Katta M, Doddamani D, Garg V, Kishor PBK, Gaur PM, Nguyen HT, Batley J, Edwards D, Sutton T and Varshney RK (2015) Prioritization of candidate genes in "QTL-hotspot" region for drought tolerance in chickpea (Cicer arietinum L.). Scientific Reports (accepted September 2015)
  5. Abberton M, Batley J, Bentley A, Bryant J, Cai H, Cockram J, Costa de Oliveira A, Cseke L, Dempewolf H, De Pace C, Edwards D, Gepts P , Greenland A, Hall A, Henry R, Hori K, Howe G, Hughes S, Humphreys M, Lightfoot D, Marshall A, Mayes S, Nguyen H, Ogbonnaya F, Ortiz R, Paterson A, Tuberosa R, Valliyodan B, Varshney R, Yano M. (2015) Global agricultural intensification during climate change: a role for genomics. Plant Biotechnology Journal (accepted August 2015)
  6. Gou L, Hattori J, Fedak G, Balcerzak M, Klassen D, Sharpe A, Visendi P, Edwards D, Tinker N, Wei Y, Chen G and Ouellet T. (2015) Development and validation of Thinopyrum elongatum expressed molecular markers specific for the long arm of chromosome 7E. Crop Science (accepted July 2015)
  7. Staňková H, Valárik M, Lapitan NLV, Berkman PJ, Batley J, Edwards D, Luo MC, Tulpová Z, Kubaláková M, Stein N, Doležel J and Šimková H. (2015) Chromosomal genomics facilitates fine mapping of a Russian wheat aphid resistance gene. Theoretical and Applied Genetics. 128 (7): 1373-1383
  8. Cai G, Yang Q, Yi B, Fan C, Zhang C, Edwards D, Batley J and Zhou Y. (2015) A bi-filtering method for processing single nucleotide polymorphism array data improves the quality of genetic map and accuracy of quantitative trait locus mapping in doubled haploid populations of polyploid Brassica napus. BMC Genomics 16, 409
  9. Pang W, Li X, Choi SR, Nguyen VD, Dhandapani V, Kim YY, Ramchiary N, Kim JG, Edwards D, Batley J, Na J, Kim HR, Lim YP. (2015) Mapping QTLs of resistance to head splitting in cabbage (Brassica oleracea L.var. capitata L). Molecular Breeding 35:126
  10. Patel DA, Zander M, Van de Wouw AP, Mason AS, Edwards D, Batley J. (2015) Population Diversity of Leptosphaeria maculans in Australia. International Journal of Biology 7 (3): 18-36
  11. Mohd-Yusoff NF, Ruperao P, Tomoyoshi NE, Edwards D, Gresshoff PM, Biswas B and Batley J. (2015) Scanning ethyl methanesulphonate effects on the whole genome of Lotus japonicus using second generation sequencing analysis. G3. 5 (4): 559-67
  12. Bayer PE, Ruperao P, Mason AS, Stiller J, Chan CKK, Hayashi S, Long Y, Meng J, Sutton T, Visendi P, Varshney RK, Batley J, Edwards D. (2015) High resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus. Theoretical and Applied Genetics 128 (6): 1039-1047.
  13. Mason M, Zhang J, Tollenaere R, Vasquez Teuber P, Dalton-Morgan J, Hu L, Yan G, Edwards D, Redden R, Batley J. (2015) High-throughput genotyping for species identification and diversity assessment in germplasm collections. Molecular Ecology Resources (Accepted January 2015).
  14. Golicz AA, Schliep M, Lee HT, Larkum AWD, Dolferus R, Batley J, Chan CKK, Sablok G, Ralph PJ, Edwards D. (2015) Genome-wide survey of the seagrass Zostera muelleri suggests modification of the ethylene signalling network. Journal of Experimental Botany. 66 (5):1489-98
  15. Lai K, Lorenc MT, Lee H, Berkman PJ, Bayer PE, Visendi P, Ruperao P, Fitzgerald TL, Zander M, Chan CK, Manoli S, Stiller J, Batley J and Edwards D. (2015) Identification and characterisation of more than 4 million inter-varietal SNPs across the group 7 chromosomes of bread wheat. Plant Biotechnology Journal 13 (1):97-104.
  16. Rosic N, Ling E, Chan K, Kaniewska P, Edwards D, Dove S, Hoegh-Guldberg O, and Lee H. (2015) Unfolding the secrets of coral-algal symbiosis. The ISME Journal. 9 (4): 844-56
  17. Golicz AA, Martinez PA, Zander M, Patel DA, Van De Wouw AP, Visendi P, Fitzgerald TL, Edwards D and Batley J. (2015) Gene loss in the fungal canola pathogen Leptosphaeria maculans. Functional and Integrative Genomics 15:189-196
  18. Rosic N, Kaniewska P, Chan K, Ling E, Edwards D, Dove D and Hoegh-Guldberg O. (2014) Early transcriptional changes in the reef-building coral Acropora aspera in response to thermal and nutrient stress. BMC Genomics 15:1052.
  19. Shin SC, Ahn DH, Kim SJ, Pyo CW, Lee H, Kim MK, Lee J, Lee JE, H. Detrich III HW, Postlethwait JH, Edwards D, Lee SG, Lee JH, Park H. The genome sequence of the Antarctic bullhead notothen reveals evolutionary adaptations to a cold environment. (2014) Genome Biology 15:468.
  20. Chalhoub B., Denoeud F., Liu S., Parkin I.A.P., Tang H., Wang X., Chiquet J., Belcram H., Tong C., Samans B., Corréa M., Da Silva C., Just J., Falentin C., Koh C.S., Le Clainche I., Bernard M., Bento P., Noel B., Labadie K., Alberti A., Charles M., Arnaud D., Guo H., Daviaud C., Alamery S., Jabbari K., Zhao M., Edger P.P., Chelaifa H., Tack D., Lassalle G., Mestiri I., Schnel N., Le Paslier M.-C., Fan G., Renault V., Bayer P.E., Golicz A.A., Manoli S., Lee T.-H., Thi V.H.D., Chalabi S., Hu Q., Fan C., Tollenaere R., Lu Y., Battail C., Shen J., Sidebottom C.H.D., Wang X., Canaguier A., Chauveau A., Bérard A., Deniot G., Guan M., Liu Z., Sun F., Lim Y.P., Lyons E., Town C.D., Bancroft I., Wang X., Meng J., Ma J., Pires J.C., King G.J., Brunel D., Delourme R., Renard M., Aury J.-M., Adams K.L., Batley J., Snowdon R.J., Tost J., Edwards D., Zhou Y., Hua W., Sharpe A.G., Paterson A.H., Guan C., Wincker P. (2014) Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science 345:950-953.
  21. Rosic N, Ling E, Chan K, Kaniewska P, Edwards D, Dove S, Hoegh-Guldberg O, and Lee H. (2014) Unfolding the secrets of coral-algal symbiosis. The ISME Journal 9(4):844-56
  22. International Wheat Genome Sequencing Consortium. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345:1251788-1251788
  23. Marcussen T., Sandve S.R., Heier L., Spannagl M., Pfeifer M., Jakobsen K.S., Wulff B.B.H., Steuernagel B., Mayer K.F.X., Olsen O.-A., International Wheat Genome Sequencing Consortium. (2014) Ancient hybridizations among the ancestral genomes of bread wheat. Science 345:1250092-1250092
  24. Pfeifer M., Kugler K.G., Sandve S.R., Zhan B., Rudi H., Hvidsten T.R., Mayer K.F.X., Olsen O.-A., International Wheat Genome Sequencing Consortium. (2014) Genome interplay in the grain transcriptome of hexaploid bread wheat. Science 345:1250091-1250091
  25. Parkin, I., Koh, C., Tang, H., Robinson, S., Kagale, S., Clarke, W., Town, C., Nixon, J., Krishnakumar, V., Bidwell, S., Denoeud, F., Belcram, H., Links, M., Just, J., Clarke, C., Bender, T., Huebert, T., Mason, A., Pires, J., Barker, G., Moore, J., Walley, P., Manoli, S., Batley, J., Edwards, D., Nelson, M., Wang, X., Paterson, A., King, G., Bancroft, I., Chalhoub, B. and Sharpe, A. (2014) Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biology 15, R77
  26. Lai K, Lorenc MT, Lee H, Berkman PJ, Bayer PE, Visendi P, Ruperao P, Fitzgerald TL, Zander M, Chan CK, Manoli S, Stiller J, Batley J and Edwards D. (2015) Identification and characterisation of more than 4 million inter-varietal SNPs across the group 7 chromosomes of bread wheat. Plant Biotechnology Journal 13 (1), 97-104
  27. Raman H, Raman R, Kilian A, Detering F, Carling J, Coombes N, Diffey S, Kadkol G, Edwards D, McCully M, Kumar P, Parkin I, Batley J, Luckett D, and Wratten N. (2014) Genome-wide delineation of natural variation for pod shatter resistance in Brassica napus. PLOS ONE. 9(7): e101673
  28. Liu S, Liu Y, Yang X, Tong C, Edwards D, Parkin IAP, Zhao M, Ma J, Yu J, SH, Wang X, Wang J, Lu K, Fan Z, Bancroft I, Yang TJ, Hu Q, Wang X, Yue Z, Li H, Yang L, Wu J, Zhou Q, Wang W, King GJ, Pires JC, Lu C, Wu Z, Sampath P, Wang Z, Guo H, Pan S, Yang L, Min J, Zhang D, Jin D, Li W, Belcram H, Tu J, Guan M, Qi C, Du D, Li J, Jiang L, Batley J, Sharpe AG, Park BS, Ruperao P, Cheng F, Waminal NE, Huang Y, Dong C, Wang L, Li J, Hu Z, Zhuang M, Huang Y, Huang J, Shi J, Mei D, Liu J, Lee TH, Wang J, Jin H, Li Z, Li X, Zhang J, L Xiao L, Zhou Y, Liu Z, Liu X, Qin R, Tang X, Liu W, Wang Y, Zhang Y, Lee J, Kim HH, Denoeud F, Xu X, Liang X, Hua W, Wang X, Wang J, Chalhoub B, Paterson AH. The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. Nature Communications. 5. DOI: 10.1038/ncomms4930
  29. Raman H, Dalton-Morgan J, Diffey S, Raman R, Alamery S, Edwards D and Batley, J. (2014) High-density SNP markers based map construction and genome-wide linkage analysis in Brassica napus. Plant Biotechnology Journal. 12:851-860
  30. Ruperao P, Chan KCK, Azam S, Karafiátová M, Hayashi S, Čížková J, Saxena RK, Šimková H, Song C, Vrána J, Chitikineni A, Visendi P, Gaur PM, Millán T, Singh KB, Taran B, Wang J, Batley J, Doležel J, Varshney RK and Edwards D. (2014) A chromosomal genomics approach to assess and validate the desi and kabuli draft chickpea genome assemblies. Plant Biotechnology Journal. 12:778-786
  31. Visendi P, Batley J, Edwards D. (2013) Next generation characterisation of cereal genomes for marker discovery. Biology 2: 1357-1377 Biology 2: 1357-1377
  32. Golicz AA, Bayer PE, Martinez PA, Lai K, Lorenc MT, Alamery S, Hayward A, Tollenaere R, Long Y, Meng J, Batley J, Edwards D. (2013) Characterising diversity in the Brassica genomes. Acta Horticulturae. 1005: 33-48
  33. Deng P, Nie X, Wang L, Cui L, Liu P, Tong W, Biradar SS, Edwards D, Berkman P, Šimková H, Doležel J, Luo M, You F, Batley J, Fleury D, Appels R, Weining S. (2013) Computational Identification and Comparative Analysis of miRNAs in Wheat Group 7 Chromosomes. Plant Molecular Biology Reporter. 1-14
  34. Kudapa H, Ramalingam A, Nayakoti S, Chen X, Zhuang WJ, Liang X , Kahl G, Edwards D, Varshney RK. (2013) Functional genomics to study stress responses in crop legumes: Progress and prospects. Functional Plant Biology. 40(12) 1221-1233
  35. Zander M, Patel DA, Van de Wouw A, Lai K, Lorenc MY, Campbell E, Hayward A, Edwards D, Raman H and Batley J. (2013) Identifying genetic diversity of avirulence genes in Leptosphaeria maculans using whole genome sequencing. Functional and Integrative Genomics. 13: 295–308
  36. Raman H, Raman R, Kilian A, Detering F, Long Y, Edwards D, Parkin IAP, Sharpe AG, Nelson MN, Larkan N, Zou J, Meng J, Aslam MN, Batley J, Cowling WA, Lydiate D. (2013) A consensus map of rapeseed (Brassica napus L) based on diversity array technology markers: Applications in genetic dissection of qualitative and quantitative traits. BMC Genomics 14: 277
  37. Varshney RK, Song C, Saxena RK, Azam S, Yu S, Sharpe AG, Cannon S, Baek J, Tar'an B, Millan T, Zhang X, Rosen B, Ramsay LD, Iwata A, Wang Y, Nelson W, Farmer AD, Gaur PM, Soderlund C, Penmetsa RV, Xu C, Bharti AK, He W, Winter P, Zhao S, Hane JK, Carrasquilla-Garcia N, Condie JA, Upadhyaya HD, Luo M, Singh NP, Lichtenzveig J, Gali KK, Rubio J, Nadarajan N, Thudi M, Dolezel J, Bansal KC, Xu X, Edwards D, Zhang G, Kahl G, Gil J, SinghKB, Datta SK, Jackson SA, Wang J, Cook D. (2013) Draft genome sequence of kabuli chickpea (Cicer arietinum): genetic structure and breeding constraints for crop improvement. Nature Biotechnology 31, 240–246
  38. Duran C, Singhania R, Raman H, Batley J, Edwards D. Predicting polymorphic EST-SSRs in silico. (2013) Molecular Ecology Resources 13 (3): 538-45
  39. Berkman, P.J., Visendi, P., Lee, H.C., Stiller, J., Manoli, S., Lorenc, M.T., Lai, K., Batley, J., Fleury, D., Šimková, H., Kubaláková, M., Weining, S., Doležel, J. and Edwards, D. (2013) Dispersion and domestication shaped the genome of bread wheat. Plant Biotechnology Journal 11 (5): 564-571
  40. Kazakoff SH, Imelfort M, Edwards D, Koehorst J, Biswas B, Batley J, Scott PT, Gresshoff PM. (2012) Capturing the biofuel wellhead and powerhouse: the chloroplast and mitochondrial genomes of the leguminous feedstock tree Pongamia pinnata. PLOS ONE e51687
  41. Raman H, Raman R, Eckermann P, Coombes N, Manoli S, Zou X, Edwards D, Meng J, Prangnell R, Stiller J, Batley J,Luckett D, Wratten N, Dennis E. (2013) Genetic and physical mapping of flowering time loci in canola (Brassica napus L.) Theoretical and Applied Genetics 126 (1): 119-132
  42. Edwards D, Batley J and Snowdon, R. (2013) Accessing complex crop genomes with next-generation sequencing. Theoretical and Applied Genetics 126 (1): 1-11
  43. Lorenc MT, Hayashi S, Stiller J, Lee H, Manoli S, Ruperao P, Visendi P, J. Berkman PJ, Lai K, Batley J and Edwards D. (2012) Discovery of single nucleotide polymorphisms in complex genomes using SGSautoSNP. Biology 1(2): 370-38
  44. Edwards D, Henry RJ and Edwards KJ. (2012) Advances in DNA sequencing accelerating plant biotechnology. Plant Biotechnology Journal. 10 (6): 621–622
  45. Hayashi S, Reid D, Lorenc M, Stiller J, Edwards D, Gresshoff PM and Ferguson BJ. (2012) Transient Nod-factor dependent gene expression in the nodulation-competent zone of soybean (Glycine max [L.] Merr.) roots. Plant Biotechnology Journal. 8: 995–1010
  46. Jiang Q, Yen SH, Stiller J, Edwards D, Scott PT and Gresshoff PM. (2012) Diversity Analysis of the Tree Legume Pongamia pinnata using PISSRs (Pongamia Inter-Simple Sequence Repeats). Journal of Plant Genome Sciences. 1 (3): 54–67
  47. Lai K, Duran C, Berkman PJ, Lorenc MT, Stiller J, Manoli S, Hayden M, Forrest K, Fleury D, Baumann U, Zander M, Mason A, Batley J, Edwards D. (2012) Single Nucleotide Polymorphism Discovery from Wheat Next Generation Sequence Data. Plant Biotechnology Journal. 10 (6): 743-749
  48. Hayward A, Vighnesh G, Delay G, Samian MR, Manoli SM, Stiller J, McKenzie M, Edwards D and Batley J. (2012) Second Generation Sequencing for Gene Discovery in the Brassicaceae. Plant Biotechnology Journal. 10 (6): 750-759
  49. Tollenaere R, Hayward A, Dalton-Morgan J, Campbell E, McLanders J, Lorenc M, Manoli S, Stiller J, Raman R, Raman H, Edwards D and Batley J. (2012) Identification and characterisation of candidate Rlm4 blackleg resistance genes in Brassica napus using next generation sequencing. Plant Biotechnology Journal. 10 (6): 709-715
  50. Edwards D, Wilcox S, Barrero RA, Fleury D, Cavanagh CR, Forrest KL, Hayden MJ, Moolhuijzen P, Keeble-Gagnère G, Bellgard MI, Lorenc MT, Shang CA, Baumann U, Taylor JM, Morell MK, Langridge P, Appels R, Fitzgerald A. (2012) Bread matters: A national initiative to profile the genetic diversity of Australian wheat. Plant Biotechnology Journal. 10 (6): 703-708
  51. Nie X, Li B, Wang L, Liu P, Biradar SS, Li T, Dolezel J, Edwards D, Luo M, Weining S. (2012) Development of chromosome-arm-specific microsatellite markers in Triticum aestivum (Poaceae) using NGS technology. American Journal of Botany. 99 (9) e369-e371
  52. Reid DE, Hayashi S, Lorenc M, Stiller J, Edwards D, Gresshoff PM, Ferguson BJ. (2012) Identification of systemic responses in soybean nodulation by xylem sap feeding and complete transcriptome sequencing reveal a novel component of the autoregulation pathway. Plant Biotechnology Journal. 10 (6): 680-689
  53. Hayward A, Dalton-Morgan J, Mason A, Zander M, Edwards D and Batley J. (2012) SNP discovery and applications in Brassica napus. Journal of Plant Biotechnology. 39: 1-12
  54. Raman R, Taylor B, Marcroft S, Stiller J, Eckermann P, Coombes N, Rehman A, Lindbeck K, Luckett D, Wratten N, Batley J, Edwards D, Wang X, Raman H. Molecular mapping of qualitative and quantitative loci for resistance to Leptosphaeria maculans causing blackleg disease in canola (Brassica napus L.) Theoretical and Applied Genetics 125: 405-415
  55. Lai K, Lorenc MT and Edwards D. (2012) Genomic databases for crop improvement. Agronomy 2: 67-73
  56. Azam S, Thakur V, Pradeep R, Shah T, Jayashree B, BhanuPrakash A, Farmer AD, Studholme DJ, May GD, Edwards D, Jones JDG and Varshney R. (2012) Coverage based consensus calling (CBCC) of short sequence reads and comparison of CBCC-results for the identification of SNPs in chickpea, a crop species without the reference genome. American Journal of Botany 99 (2): 186-192
  57. Hayward A, McLanders J, Campbell E, Edwards D and Batley J. (2012) Genomic advances will herald new insights into the Brassica:Leptosphaeria maculans pathosystem. Plant Biology 14 (1): 1-10
  58. Berkman PJ, Lai K, Lorenc MT and Edwards D. Next generation sequencing applications for wheat crop improvement. (2012) American Journal of Botany 99 (2): 365-371
  59. Lee H, Lai K, Lorenc MT, Imelfort M, Duran C and Edwards D. (2012) Bioinformatics tools and databases for analysis of next generation sequence data. Briefings in Functional Genomics 11 (1), 12-24
  60. Lai K, Berkman PJ, Lorenc MT, Duran C, Smits L, Manoli S, Stiller J and Edwards D. (2012) WheatGenome.info: An integrated database and portal for wheat genome information. Plant and Cell Physiology 53(2): e2(1–7)
  61. Berkman PJ, Skarshewski A, Manoli S, Lorenc MT, Stiller J, Smits L, Lai K, Campbell E, Kubaláková M, Šimková H, Batley J, Doležel J, Pilar Hernandez P, and Edwards D. (2012) Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation. Theoretical and Applied Genetics 3: 423-432
  62. Rosic N, Kaniewska P, Ling E, Edwards D, Dove S, Hoegh-Guldberg O. (2011) Transcriptomics of the Coral-Algal Symbiosis in Response to Environmental Stress. European Journal of Phycology 46, 97
  63. The Brassica rapa Genome Sequencing Project Consortium. (2011) The genome of the mesopolyploid crop species Brassica rapa. Nature Genetics 43: 1035-1040
  64. Berkman PJ, Skarshewski A, Lorenc MT, Lai K, Duran C, Ling EYS, Stiller J, Smits L, Imelfort M, Manoli S, McKenzie M, Kubaláková M, Šimková H, Batley J, Fleury D, Doležel J and Edwards D. (2011) Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS. Plant Biotechnology Journal 9 (7): 768-775
  65. Mun JH, Kwon SJ, Seol YJ, Kim JA, Jin M, Kim JS, Lim MH, Lee SI, Hong JK, Park TH, Lee SC, Kim BJ, Seo MS, Baek S, Lee MJ, Shin JY, Hahn JH, Hwang YJ, Lim KB, Park JY, Lee J, Yang TJ, Yu HJ, Choi SR, Ramchiary N, Lim YP, Fraser F, Drou N, Soumpourou E, Trick M, Bancroft I, Parkin IAP, Batley J, Edwards D and Park BS. (2010) Sequence and structure of Brassica rapa chromosome A3. Genome Biology 11: R94
  66. Koo DH, Hong CP, Batley J, Chung YS, Edwards D, Bang JW, PhD; Hur Y and Lim YP. (2010) Rapid Divergence of Repetitive DNAs in Brassica Relatives. Genomics 97(3): 173-185
  67. Duran C, Eales D, Marshall D, Imelfort M, Stiller J, Berkman P, Clark T, McKenzie M, Appleby N, Batley J, Basford K, and Edwards D. (2010) Future tools for association mapping in crop plants. Genome 53: 1017-1023
  68. Marshall DJ, Hayward A, Eales D, Imelfort M, Stiller J, Berkman PJ, Clark T, McKenzie M, Lai K, Duran C, Batley J and Edwards D. (2010) Targeted identification of genomic regions using TAGdb. Plant Methods 6:19
  69. Duran C, Boskovic Z, Imelfort M, Batley J, Hamilton NA and Edwards D. (2010) CMap3D: A 3D visualisation tool for comparative genetic maps. Bioinformatics 26 (2): 273-274
  70. Edwards D and Batley J. (2010) Plant genome sequencing: applications for crop improvement. Plant Biotechnology Journal 8: 2–9
  71. Kaur S, Cogan N.O.I, Ye G, Baillie R.C, M. L. Hand M.L, Ling A.E., Mcgearey A.K., Kaur J, Hopkins C.J, Todorovic M, Mountford H, Edwards D, Batley J, Burton W, Salisbury P, Gororo N, Marcroft S, Kearney G, Smith K.F, Forster J.W, Spangenberg G.C. (2009) Genetic map construction and QTL mapping of resistance to blackleg (Leptosphaeria maculans) disease in Australian canola (Brassica napus L.) cultivars. Theoretical and Applied Genetics 120 (1): 71-83
  72. Imelfort M and Edwards D. (2009) De novo sequencing of plant genomes using second-generation technologies. Briefings in Bioinformatics 10: 609-618
  73. Batley J and Edwards D. (2009) Genome sequence data: management, storage, and visualization. Biotechniques 46:333-336
  74. Duran C, Appleby N, Vardy M, Imelfort M, Edwards D and Batley J. (2009) Single Nucleotide Polymorphism Discovery in Barley using AutoSNPdb. Plant Biotechnology Journal 7 (4): 326 – 333
  75. Imelfort M, Duran C, Batley J and Edwards D. (2009) Discovering genetic polymorphisms in next generation sequencing data. Plant Biotechnology Journal 7 (4): 312 – 317
  76. Duran C, Appleby N,, Edwards D and Batley J. (2009) Molecular genetic markers: discovery, applications, data storage and visualisation. Current Bioinformatics 4: 16-27
  77. Duran C, Appleby N, Clark T, Wood D, Imelfort M, Batley J and Edwards D. (2009) AutoSNPdb: An Annotated Single Nucleotide Polymorphism Database for Crop Plants. Nucleic Acids Research 37: 951–953
  78. Choi SR, Teakle GR, Plaha P, Kim JH, Allender CJ, Beynon E, Piao ZY, Soengas P, Han TH, King GJ, Barker GC, Hand P, Lydiate DJ, Batley J, Edwards D, Koo DH, Bang JW, Park BS and Lim YP. (2007) The reference genetic linkage map for the multinational Brassica rapa genome sequencing project. Theoretical and Applied Genetics 115 (6): 777-792
  79. Lim GAC, Jewell EG, Li X, Erwin TA, Love C, Batley J, Spangenberg G and Edwards D. (2007) A Comparative Map Viewer Integrating Genetic Maps for Brassica and Arabidopsis. BMC Plant Biology 7: 40
  80. Hong CP, Piao ZY, Kang TW, Batley J, Yang TJ, Hur YK, Bhak J, Edwards D and Lim YP. (2007) Genomic distribution of Simple Sequence Repeats in Brassica rapa. Molecules and Cells 23 (3): 349-356
  81. Batley J, Hopkins CJ, Cogan NOI, Hand M, Jewell E, Kaur J, Kaur S, Li X, Ling AE, Love C, Mountford H, Todorovic M, Vardy M, Walkiewicz M, Spangenberg GC and Edwards D. (2007) Identification and characterisation of Simple Sequence Repeat (SSR) markers from Brassica napus expressed sequences. Molecular Ecology Notes 7: 886–889.
  82. Hopkins CJ, Cogan NOI, Hand M, Jewell E, Kaur J, Li X, Lim GAC, Ling AE, Love C, Mountford H, Todorovic M, Vardy M, Spangenberg GC, Edwards D and Batley J. (2007) Sixteen new simple sequence repeat markers from Brassica juncea expressed sequences and their cross-species amplification. Molecular Ecology Notes 7: 697-700
  83. Ling AE, Kaur J, Burgess B, Hand M, Hopkins CJ, Li X, Love CG, Vardy M, Walkiwiecz M, Spangenberg G, Edwards D and Batley J. (2007) Characterisation of Simple Sequence Repeat markers derived in silico from Brassica rapa Bacterial Artificial Chromosome sequences and their application in Brassica napus. Molecular Ecology Notes 7: 273-277
  84. Erwin T, Jewell E, Love C, Lim G, Li X, Chapman R, Batley J, Stajich J, Mongin E, Stupka E, Ross B, Spangenberg G and Edwards D. (2007) BASC: an integrated bioinformatics system for Brassica research. Nucleic Acids Research 35: D870–D873
  85. Donnison IS, Gay AP, Thomas H, Edwards KJ, Edwards D, James CL, Thomas AM, Ougham HJ. (2007) Modification of nitrogen remobilisation, grain fill and leaf senescence in maize (Zea mays L.) by transposon insertional mutagenesis. New Phytologist 173: 481-494
  86. Burgess B, Mountford H, Hopkins CJ, Love C, Ling AE, Spangenberg G, Edwards D and Batley J. (2006) Identification and characterisation of Simple Sequence Repeat (SSR) markers derived in silico from Brassica oleracea genome shotgun sequences. Molecular Ecology Notes 6: 1191-1194
  87. Hong CP, Plaha P, Koo DH, Yang TJ, Choi SR, Lee YK, Uhm T, Bang JW, Edwards D, Bancroft I, Park BS, Lee J, and Lim YP. (2006) A Survey of the Brassica rapa Genome through BAC-End Sequence Analysis, and Comparative Analysis with Arabidopsis thaliana. Molecules and Cells 22: 300-307
  88. Philippar K, Büchsenschütz K, Edwards D, Löffler J, Lüthen H, Kranz E, Edwards KJ and Hedrich R. (2006) The auxin-induced K+ channel gene Zmk1 in maize functions in coleoptile growth and is required for embryo development. Plant Molecular Biology 61: 757-768
  89. Jewell E, Robinson A, Savage D, Erwin T, Love CG, Lim GAC, Li X, Batley J, Spangenberg GC and Edwards D. (2006) SSR Primer and SSR Taxonomy Tree: Biome SSR discovery. Nucleic Acids Research 34: W656–W659
  90. Love C, Logan E, Erwin T, Spangenberg G and Edwards D. (2006) Analysis of the Brassica A and C Genomes and Comparison with the Genome of Arabidopsis thaliana. Acta Horticulturae 706: 99-104
  91. Love C, Logan E, Erwin T, Kaur J, Lim GAC, Hopkins C, Batley J, James N, May S, Spangenberg G and Edwards D. (2006) Integrating and interrogating diverse Brassica data within an EnsEMBL structured database. Acta Horticulturae 706: 77-82
  92. Hopkins C, Mogg R, Gororo N, Salisbury PA, Burton WA, Love C, Spangenberg GC, Edwards D and Batley J. (2006) An assessment of genetic diversity within and between Brassica napus and Brassica juncea lines from international germplasm collections. Acta Horticulturae 706: 115-119
  93. Keniry A, Hopkins CJ, Jewell E, Morrison B, Spangenberg GS, Edwards D and Batley J. (2006) Identification and characterisation of Simple Sequence Repeat (SSR) markers from Fragaria x ananassa expressed sequences. Molecular Ecology Notes 6: 319-322
  94. Felitti S, Shields K, Ramsperger M, Tian P, Sawbridge T, Webster T, Logan E, Erwin T, Forster J, Edwards D and Spangenberg G. (2006) Transcriptome analysis of Neotyphodium and Epichloë grass endophytes. Fungal Genetics and Biology 43: 465-475
  95. Sexton A, Cozijnsen A, Keniry A, Logan E, Love C, Batley J, Edwards D and Howlett B. (2006) Transcription profile of genes from three developmental stages of the plant pathogen Sclerotinia sclerotiorum. FEMS Microbiology Letters 258: 150-160
  96. Savage D, Batley J, Erwin T, Logan E, Love CG, Lim GAC, Mongin E, Barker GLA, Spangenberg GC and Edwards D. (2005) SNPServer: A Realtime SNP Discovery tool. Nucleic Acids Research 33: D656-D659
  97. Mortimer J, Batley J, Love C, Logan E and Edwards D. (2005) Simple Sequence Repeat (SSR) and GC distribution in the Arabidopsis thaliana genome. Journal of Plant Biotechnology 7: 17-25
  98. Love C, Robinson A, Lim G, Hopkins C, Batley J, Barker G, Spangenberg G and Edwards D. (2005) Brassica ASTRA: An Integrated Database for Brassica Genomic Research. Nucleic Acids Research 33: W493-W495
  99. Robinson AJ, Love CG, Batley J, Barker G and Edwards D. (2004) Simple Sequence Repeat Marker Loci Discovery using SSR Primer. Bioinformatics 20: 1475-1476
  100. Wilson ID, Barker GLA, Beswick RW, Shepherd SK, Lu C, Coghill JA, Edwards D, Owen P, Lyons R, Parker JS, Lenton JR, Holdsworth MJ, Shewry PR and Edwards KJ. (2004) A transcriptomics resource for wheat functional genomics. Plant Biotechnology Journal 2: 495-506
  101. Edwards D and Batley J. (2004) Plant Bioinformatics: From Genome to Phenome. Trends in Biotechnology 22: 232-237
  102. Love CG, Batley J, Lim G, Robinson AJ, Savage D, Singh D, Spangenberg GC, and Edwards D. (2004) New computational tools for Brassica genome research. Comparative and Functional Genomics 5: 276-280
  103. Love CG, Batley J and Edwards D. (2003) Applied Computational Tools for Crop Genome Research. Journal of Plant Biotechnology 5: 193-195
  104. Batley J, Barker G, O'Sullivan H, Edwards KJ and Edwards D. (2003) Mining for Single Nucleotide Polymorphisms and Insertions/Deletions in Maize Expressed Sequence Tag Data. Plant Physiology 132: 84-91
  105. Batley J, Mogg R, Edwards D, O’Sullivan H and Edwards KJ. (2003) A high-throughput SNuPE assay for genotyping SNPs in the flanking regions of Zea mays sequence tagged simple sequence repeats. Molecular Breeding 11: 111-120
  106. Barker G, Batley J, O'Sullivan H, Edwards KJ and Edwards D. (2003) Redundancy Based Detection of Sequence Polymorphisms in Expressed Sequence Tag Data using AutoSNP. Bioinformatics 19: 421-422
  107. Edwards D, Coghill J, Batley J, Holdsworth M and Edwards KJ. (2002) Amplification and detection of transposon insertion flanking sequences using fluorescent MuAFLP. Biotechniques 32: 1090-1097
  108. Edwards D, Stevenson D, Forsyth A, Hegarty M, Batley J, Holdsworth M and Edwards KJ. (2002) Identification of transposon-tagged maize genes displaying homology to arrayed cDNA clones using Mutator insertion display. Genome letters 1: 48-55
  109. Mogg R, Batley J, Hanley S, Edwards D, O’Sullivan H and Edwards KJ. (2002) Characterisation of the flanking regions of Zea Mays microsatellites reveals a large number of useful sequence polymorphisms. Theoretical and Applied Genetics 105: 532-543
  110. O’ Sullivan D, Edwards D, Edwards KJ. Maize Genomics. AgBiotechNet (2000) 2
  111. Hanley S, Edwards D, Stevenson D, Haines S, Hegarty M, Schuch W, Edwards KJ. Identification of transposon tagged genes by the random sequencing of Mutator-tagged DNA fragments from Zea mays. Plant Journal (2000) 23 (4):557-566
  112. Edwards D, Murray JAH, Smith AG. (1998) Multiple genes encoding the conserved CCAAT-box transcription factor complex are expressed in Arabidopsis. Plant Physiology 117 (3): 1015-1022
  113. Edwards KJ, Thompson H, Edwards D, DeSaizeu A, Sparks C, Thompson JA, Greenland AJ, Eyers M and Schuch W. (1992) Construction and Characterisation of a Yeast Artificial Chromosome Library Containing 3 Haploid Maize Genome Equivalents. Plant Molecular Biology 19: (2) 299-308

CONFERENCE PAPERS:

  1. Batley J, Edwards D, Spangenberg G, Burgess BR, Burton W, Erwin T, Hand M, Hopkins C, Howlett B, Jewell E, Kaur J, Keniry A, Li X, Love CG, Marcroft S, Mountford H, Salisbury P and Walkiewicz M. (2005) Development of molecular markers for implementation in Australian Brassica Improvement. In: 14th Australian Research Assembly on Brassicas. of a conference, Port Lincoln 2005. Ed. T Potter. SARDI, Primary Industries and Resources South Australia, pp 65-69
  2. Edwards D, Batley J, Spangenberg G, Burgess BR, Erwin T, Hand M, Hopkins C, Jewell E, Keniry A, Li X, Love CG, Mountford H and Walkiewicz M. (2005) The Multinational Brassica Genome Project. In: 14th Australian Research Assembly on Brassicas. Port Lincoln 2005, Proceedings Ed. T Potter. SARDI, Primary Industries and Resources South Australia, pp 70-72
  3. Batley J and Edwards D. (2004) Molecular Tools for Plant Biology. In: Proceedings of Vision for Practical Use of Biotechnology. The Korean Society of Plant Biotechnology. Korea pp 19-24
  4. Batley J, Vecchies A, Mogg R, Bond J, Cogan N, Hopkins C, Gororo N, Marcroft S, Forster J, Spangenberg G and Edwards D. (2003) A study of genetic diversity among Brassica napus and Brassica juncea germplasm collections using Simple Sequence Repeat (SSR) markers. Thirteen Biennial Australian Research Assembly on Brassicas. Proceedings of a conference, Tamworth, New South Wales. pp 84-86
  5. Edwards D. (2003) Applied Computational Tools for Crop Genome Research. In: Proceedings of Development of Core Biotechnology for Next Generation. The Korean Society of Plant Biotechnology. Korea 33-34

OTHER PUBLICATIONS:

  1. Li X, Jewell E, Erwin TA, Lim GAC, Love CG, Batley J, Spangenberg GC and Edwards D. (2007) Brassica Bacterial Artificial Chromosome (BAC) and Gene Annotator. Cruciferae Newsletter 27
  2. Ling A, Hopkins C, Burton W, Hand M, Kaur S, McGearey A, Kaur J, Love C, Salisbury P, Todorovic M, Vardy M, Walkiewicz M, Spangenberg G, Edwards D and Batley J. (2007) Development of Molecular Markers for Implementation in the Australian National Brassica Improvement Program. Cruciferae Newsletter 27
  3. Lim GAC, Jewell EG, Li X, Erwin TA, Love C, Spangenberg GC and Edwards D. (2007) CMap: A Comparative Mapping Tool for Brassica. Cruciferae Newsletter 27
  4. Erwin TA, Jewell E, Love CG, Xi Li, Lim GAC, Chapman R, Spangenberg G, and Edwards D. (2007) Brassica BASC: An Integrated Bioinformatics System for Brassica Research. Cruciferae Newsletter 27
  5. Kaur J, Webster T, Chapman R, Batley J, Salisbury P, Spangenberg GC and Edwards D. (2007) Gene Expression Studies in Canola in Response to Blackleg (Leptosphaeria maculans) Infection. Cruciferae Newsletter 27
  6. Savage D, Logan E, Erwin T, Robinson A, Love CG, Barker G, Batley J and Edwards D. (2007) Real-time mining of maize genome data for simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) molecular genetic markers. Maize Newsletter 79
  7. Swarbreck D, O’Sullivan D, Ripoll PJ, Edwards D, Edwards KJ and Theodoulou F. (2002) Unravelling the MRP family in monocots. Comparative Biochemistry and Physiology A: Molecular & Integrative Physiology 32: S1
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