Publications JB

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Publications

BOOKS:

1. Oilseed Brassicas Eds. Edwards D, Batley J and Parkin I. 2011. Science Publishers Inc (USA), 440pp

2. Plant Genotyping Ed. Batley J. 2015. Human Press (USA), 315pp

3. Plant Genomics and Climate Change. Eds. Edwards D, Batley J 2016. Springer (USA), 200pp

BOOK CHAPTERS:

1. Visendi P, Batley J and Edwards D. Next generation sequencing and germplasm resources. In: Advances in genomics of plant genetic resources (Eds. Tuberosa R, Graner A and Frison E). In press (accepted April 2012)

2. Edwards D, Zander M, Dalton-Morgan J and Batley J. 2012. New technologies for ultra-high throughput genotyping in plant taxonomy. In: Molecular Plant Taxonomy (Ed. Besse P). In press (accepted April 2012)

3. Duran C, Boskovic Z, Batley J and Edwards D. 2011. Brassica Bioinformatics. In: Vegetable Brassicas (Ed. Sadowski J) Science Publishers Inc (USA), pp406-418

4. Duran C, Edwards D and Batley J. 2009. Molecular Marker Discovery and Genetic map Visualisation. In: Applied Bioinformatics (Eds. Edwards D, Hanson D and Stajich J). Springer (USA), pp165-189

5. Appleby N, Edwards D and Batley J. 2009. New technologies for ultra-high throughput genotyping in plants. In: Plant Genomics. (Eds Somers DJ, Langridge P, and Gustafson JP) Humana Press (USA), pp19-39

6. Duran C, Edwards D and Batley J.2009. Genetic maps and the use of synteny. In: Plant Genomics. (Eds Somers DJ, Langridge P, and Gustafson JP) Humana Press (USA), pp41-55

7. Imelfort M, Batley J, Grimmond S and Edwards D. 2009. Genome sequencing approaches and successes. In: Plant Genomics. (Eds Somers DJ, Langridge P, and Gustafson JP) Humana Press (USA), pp345-358

8. 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. D. Posada) Humana Press (USA) pp303-322

9. Batley J and Edwards D. 2008. Bioinformatics: Fundamentals and Applications in Plant Genetics and Breeding. In: Principles and Practices of Plant Molecular Mapping and Breeding. (Eds. C. Kole and AG Abbott). Science Publishers, Inc., (USA) pp 269-302

10. 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. D. Edwards) Humana Press (USA), pp. 473-494

11. Edwards D, Forster JW, Chagné D and Batley J. 2007. What are SNPs? In: Association Mapping in Plants (Eds. NC Oraguzie, EHA Rikkerink, SE Gardiner and HN De Silva) Springer NY, pp 41-52

12. Edwards D, Batley J, Cogan NOI, Forster JW and Chagné D. 2007. Single Nucleotide Polymorphism Discovery. In: Association Mapping in Plants (Eds. NC Oraguzie, EHA Rikkerink, SE Gardiner and HN De Silva) Springer NY, pp 53-76

13. Chagné D, Batley J, Edwards D, and Forster JW. 2007. Single Nucleotide Polymorphisms genotyping in plants. In: Association Mapping in Plants (Eds. NC Oraguzie, EHA Rikkerink, SE Gardiner and HN De Silva) Springer NY, pp 77-94

14. Batley J and Edwards D. 2007. SNP applications in plants. In: Association Mapping in Plants (Eds. NC Oraguzie, EHA Rikkerink, SE Gardiner and HN De Silva) Springer NY, pp 95-102

15. Edwards D, Salisbury PA, Burton WA, Hopkins CJ and Batley J. 2007. Indian mustard. In Genome Mapping and Molecular Breeding in Plants. Vol II Oilseeds (Ed. C Kole) Springer Berlin, pp 179-210

16. Spangenberg GC, Forster JW, Edwards D, John U, Mouradov A, Emmerling M, Batley J, Felitti S, Cogan NOI, Smith KF and Dobrowolski M. 2004. Future Directions in the Molecular Breeding of Forage and Turf. In: Molecular Breeding for Genetic Improvement of Forage Crops and Turf (Ed. MO Humphreys) Wageningen Academic Publishers, pp 83-97

17. Forster JW, Jones ES, Batley J and Smith KF. 2004. Molecular marker-based genetic analysis of pasture and turf grasses. In: Molecular Breeding of Forage and Turf (Eds. A Hopkins., ZY Wang, M Sledge and RE Barker). Kluwer Academic Press, pp 197-239

18. van Zijll de Jong E, Bannan NR, Batley J, Guthridge KM, Spangenberg GC, Smith KF and Forster JW. 2004. Genetic diversity in the perennial ryegrass fungal endophyte Neotyphodium lolii. In: Molecular Breeding of Forage and Turf (Ed A Hopkins., ZY Wang, M Sledge and RE Barker). Kluwer Academic Press, pp 155-165

JOURNAL ARTICLES:

2016

1. Blum A, Benfield AH, Stiller J, Kazan K, Batley J, Gardiner DM. 2016. High-throughput FACS-based mutant screen identifies a gain-of-function allele of the Fusarium graminearum adenylyl cyclase causing deoxynivalenol over-production. Fungal Genetics and Biology 90: 1-11

2. Edwards D and Batley J. 2016. The application of genomics and bioinformatics to accelerate crop improvement in a changing climate. Current Opinion in Plant Biology 30: 78-81.

3. Kettle AJ, Carere J, Batley J, Manners JM, Kazan K and Gardiner D. 2016. The Fdb3 transcription factor of the Fusarium detoxification of benzoxazolinone gene cluster is required for MBOA but not BOA degradation in Fusarium pseudograminearum. Fungal Genetics and Biology 88: 44-53

4. Gupta M, Mason AS, Batley J, Bharti S, Banga S and Banga SS. 2016. Molecular-cytogenetic characterisation of C-genome chromosome substitution lines in Brassica juncea (L.) Czern and Coss. Theor. & Appl. Genet. 129:1153-1166

5. Visendi P, Berkman PJ, Hayashi S, Golicz AA, Bayer PE, Ruperao P, Hurgobin B, Montenegro J, Chan C-K.K, Staňková H, Batley J, Šimková H, Doležel J and Edwards D. 2016. An efficient approach to BAC based assembly of complex genomes. Plant Methods. 12:1

6. Subramaniam G, Trusov Y, Encina CL, Hayashi S, Batley J and Botella JR. 2016. Type B heterotrimeric G protein γ subunit regulates auxin and ABA signaling in tomato. Plant Physiology (accepted Feb. 2016)

7. Nelson M, Helliwell C, Taylor C, Siddique K, Chen S, Raman H, Batley J and Cowling W. 2016. Can genomics assist the phenological adaptation of canola to new and changing environments? Crop and Pasture Science (accepted Dec.2015)

8. Staňková H, Hastie AR, Chan S, Vrana J, Tulpová Z, Kubaláková M, Visendi P, Hayashi S, Luo MC, Batley J, Edwards D, Doležel J and Šimková H. 2016. BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes. Plant Biotech. J. (accepted Dec. 2015)

9. Golicz AA, Batley J and Edwards D. 2016. Towards plant pangenomes. Plant Biotechnology Journal. (accepted November 2015)

10. 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 and Yano M. 2015 Global agricultural intensification during climate change: a role for genomics. Plant Biotech. J. (accepted August 2015)

11. Mason AS and Batley J. 2015. Creating new interspecific hybrid and polyploid crops. Trends in Biotechnology 33: 436-441.

12. Kettle AJ, Carere J, Batley J, Benfield AH, Manners JM, Kazan K and Gardiner D. 2016. A γ-lactamase from cereal infecting Fusarium spp. catalyses the first step in the degradation of the benzoxazolinone class of phytoalexins. Fungal Genetics and Biology 83: 1-9

13. Munir F, Hayashi S, Batley J, Naqvi SMS and Mahmood T. 2016. Germin-like protein 2 gene promoter from rice is responsive to fungal pathogens in transgenic potato plants. Funct. & Int. Gen 16:19-27


2015

14. Mason AS, Takahira J, Atri C, Samans B, Hayward A, Cowling WA, Batley J and Nelson MN. 2015. Microspore culture reveals complex meiotic behaviour in a trigenomic Brassica hybrid. BMC Plant Biology 15: 173

15. 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

16. Patel DA, Zander M, Van de Wouw AP, Mason AS, Edwards D and Batley J. 2015. Population Diversity of Leptosphaeria maculans in Australia. International Journal of Biology 7: 18

17. Kettle AJ, Batley J, Benfield AH, Manners JM, Kazan K and Gardiner D. 2015. Degradation of the benzoxazolinone class of phytoalexins is important for virulence of Fusarium pseudograminearum towards wheat. Molecular Plant Pathology 16: 946-962

18. 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: 1373-1383

19. Pang W, Li X, Choi SR, Nguyen VD, Dhandapani V, Kim YY, Ramchiary N, Kim JG, Edwards D, Batley J, Na J, Kim H and Lim YP. 2015. Mapping QTLs of resistance to head splitting in cabbage (Brassica oleracea L. var. capitata L.). Molecular Breeding 35: 1-12

20. Li L, Long Y, Zhang L, Dalton-Morgan J, Batley J, Yu L, Meng J and Li M. 2015. Genome wide analysis of flowering time trait in multiple environments via high-throughput genotyping technique in Brassica napus L. PloS One 10: e0119425.

21. 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: 559-567

22. Bayer PE, Ruperao P, Mason AS, Stiller J, Chan CKK, Hayashi S, Long Y, Meng J, Sutton T, Visendi P, Varshney RK, Batley J and Edwards D. 2015 High resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus. Theor. & Appl. Genet.128: 1039-1047

23. Mason AM, Zhang J, Tollenaere R; Vasquez Teuber P, Dalton-Morgan J, Hu L, Yan G, Edwards D, Redden R and Batley J. 2015 High-throughput genotyping for species identification and diversity assessment in germplasm collections. Molecular Ecology Resources 15:1091-1101

24. Golicz AA, Schliep M, Lee HT, Larkum AWD, Dolferus R, Batley J, Chan CKK, Sablok G, Ralph PJ and Edwards D. 2015. Genome-wide survey of the seagrass Zostera muelleri suggests modification of the ethylene signalling network. Journal of Experimental Botany 66: 1489-1498

25. Chambers K, Lowe RGT, Howlett BJ, Zander M, Batley J, Van de Wouw AP and Elliott C. 2015.Next-generation genome sequencing can be used to rapidly characterise sequences flanking T-DNA insertions in random insertional mutants of Leptosphaeria maculans. Fungal Biology and Biotechnology 1:10

26. 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. Funct. & Int. Gen. 15: 189-196.

27. Dalton-Morgan J, Hayward A, Alamery S, Tollenaere R, Mason AS, Campbell E, Patel D, Lorenc MT, Yi B, Long Y, Meng J, Raman R, Raman H, Lawley C, Edwards D and Batley J. 2014. A high-throughput SNP array in the amphidiploid species Brassica napus shows diversity in resistance genes. Funct. & Int. Gen 14: 643-655.

28. Cai G, Yang Q, Yi B, Fan C, Edwards D, Batley J and Zhou Z. 2014. A complex recombination pattern in the genome of allotetraploid Brassica napus as revealed by a high-density genetic map. PloS one 9: e109910

29. Lai K, Lorenc M, Lee H, Berkman P, Bayer P, Visendi P, Ruperao P, Fitzgerald T, Zander M, Chan K, Manoli S, Stiller J, Batley J and Edwards D. 2015 Identification and characterisation of more than 4 million SNPs across the group 7 chromosomes of bread wheat. Plant Biotechnology Journal. 13: 97-104


2014

30. 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

31. Marcussen T, Sandve SR, Heier L, Spannagl M, Pfeifer M, Rogers J, Doležel J, Pozniak C, Eversole K, Feuillet C, Gill B, Friebe B, Lukaszewski AJ, Sourdille P, Endo TR, Kubaláková M, Číhalíková J, Dubská Z, Vrána J, Šperková R, Šimková H, Febrer M, Clissold L, McLay K, Singh K, Chhuneja P, Singh NK, Khurana J, Akhunov E, Choulet F, Alberti A, Barbe V, Wincker P, Kanamori H, Kobayashi F, Itoh T, Matsumoto T, Sakai H, Tanaka T, Wu J, Ogihara Y, Handa H, Maclachlan PR, Sharpe A, Klassen D, Edwards D, Batley J, Lien S, Caccamo M, Ayling S, Ramirez-Gonzalez RH, Clavijo BJ, Wright J, Martis MM, Mascher M, Chapman J, Poland JA, Scholz U, Barry K, Waugh R, Rokhsar DS, Muehlbauer GJ, Stein N, Gundlach H, Zytnicki M, Jamilloux V, Quesneville H, Wicker T, Faccioli P, Colaiacovo M, Stanca AM, Budak H, Cattivelli L, Glover N, Pingault L, Paux E, Sharma S, Appels R, Bellgard M, Chapman B, Nussbaumer T, Bader KC, Rimbert H, Wang S, Knox R, Kilian A, Alaux M, Alfama F, Couderc L, Guilhot N, Viseux C, Loaec M, Keller B, Praud S, Jakobsen KS, Wulff BBH, Steuernagel B, Mayer KFX and Olsen O-A. 2014. Ancient hybridisations among the ancestral genomes of bread wheat. Science 345:1250092

32. Chalhoub B, Denoeud F, Liu S, Parkin IAP, Tang H, Wang X, Chiquet J, Belcram H, Tong C, Samans B, Corréa M, Da Silva C, Just J, Falentin C, Koh CS, 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 PP, Chelaifa H, Tack D, Lassalle G, Mestiri I, Schnel N, Le Paslier M-C, Fan G, Renault V, Bayer PE, Golicz AA, Manoli S, Lee T-H, Thi VHD, Chalabi S, Hu Q, Fan C, Tollenaere R, Lu Y, Battail C, Shen J, Sidebottom CHD, Wang X, Canaguier A, Chauveau A, Bérard A, Deniot G, Guan M, Liu Z, Sun F, Lim YP, Lyons E, Town CD, Bancroft I, Wang X, Meng J, Ma J, Pires JC, King GJ, Brunel D, Delourme R, Renard M, Aury J-M, Adams KL, Batley J, Snowdon RJ, Tost J, Edwards D, Zhou Y, Hua W, Sharpe AG, Paterson AH, Guan C and Wincker P. 2014 Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science 345:950-953

33. Pfeifer M, Kugler KG, Sandve SR, Zhan B, Rudi H, Hvidsten TR, Rogers J, Doležel J, Pozniak C, Eversole K, Feuillet C, Gill B, Friebe B, Lukaszewski AJ, Sourdille P, Endo TR, Kubaláková M, Číhalíková J, Dubská Z, Vrána J, Šperková R, Šimková H, Febrer M, Clissold L, McLay K, Singh K, Chhuneja P, Singh NK, Khurana J, Akhunov E, Choulet F, Alberti A, Barbe V, Wincker P, Kanamori H, Kobayashi F, Itoh T, Matsumoto T, Sakai H, Tanaka T, Wu J, Ogihara Y, Handa H, Maclachlan PR, Sharpe A, Klassen D, Edwards D, Batley J, Lien S, Caccamo M, Ayling S, Ramirez-Gonzalez RH, Clavijo BJ, Wright J, Martis MM, Mascher M, Chapman J, Poland JA, Scholz U, Barry K, Waugh R, Rokhsar DS, Muehlbauer GJ, Stein N, Gundlach H, Zytnicki M, Jamilloux V, Quesneville H, Wicker T, Faccioli P, Colaiacovo M, Stanca AM, Budak H, Cattivelli L, Glover N, Pingault L, Paux E, Sharma S, Appels R, Bellgard M, Chapman B, Nussbaumer T, Bader KC, Rimbert H, Wang S, Knox R, Kilian A, Alaux M, Alfama F, Couderc L, Guilhot N, Viseux C, Loaec M, Keller B, Praud S, Mayer KFX and Olsen O-A. 2014. Genome interplay in the grain transcirptome of hexaploid bread wheat. Science 345:1250091

34. Mayer KFX, Rogers J, Doležel J, Pozniak C, Eversole K, Feuillet C, Gill B, Friebe B, Lukaszewski AJ, Sourdille P, Endo TR, Kubaláková M, Číhalíková J, Dubská Z, Vrána J, Šperková R, Šimková H, Febrer M, Clissold L, McLay K, Singh K, Chhuneja P, Singh NK, Khurana J, Akhunov E, Choulet F, Alberti A, Barbe V, Wincker P, Kanamori H, Kobayashi F, Itoh T, Matsumoto T, Sakai H, Tanaka T, Wu J, Ogihara Y, Handa H, Maclachlan PR, Sharpe A, Klassen D, Edwards D, Batley J, Lien S, Caccamo M, Ayling S, Ramirez-Gonzalez RH, Clavijo BJ, Wright J, Martis MM, Mascher M, Chapman J, Poland JA, Scholz U, Barry K, Waugh R, Rokhsar DS, Muehlbauer GJ, Stein N, Gundlach H, Zytnicki M, Jamilloux V, Quesneville H, Wicker T, Faccioli P, Colaiacovo M, Stanca AM, Budak H, Cattivelli L, Glover N, Pingault L, Paux E, Sharma S, Appels R, Bellgard M, Chapman B, Nussbaumer T, Bader KC, Rimbert H, Wang S, Knox R, Kilian A, Alaux M, Alfama F, Couderc L, Guilhot N, Viseux C, Loaec M, Keller B and Praud S. A chromosome based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345:1251788

35. Parkin IAP, Koh C, Tang H, Robinson SJ, Kagale S, Clarke WE, Town CD, Nixon J, Krishnakumar V, Bidwell SL, Denoeud F, Belcram H, Links MG, Just J, Clarke C, Bender T, Huebert T, Mason AS, Pires JC, Barker G, Moore J, Walley PG, Manoli S, Batley J, Edwards D, Nelson MN, Wang X, Paterson AH, King G, Bancroft I, Chaloub B and Sharpe AG. 2014 Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biology 15:R77

36. Raman H, Raman R, Kilian A, Detering F, Carling J, Coombes N, Diffey S, Kadkol G, Edwards D, McCully M, Ruperao 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: e101673

37. Liu S, Liu Y, Yang X, Tong C, Edwards D, A. P. 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 and Paterson AH. 2014 The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. Nature Communications 5:3930

38. Ruperao P, Chan C-K K, Azam S, Karafiatova M, Hayashi S, Cizkova J, Saxena RK, Simkova H, Song C, Vrana J, Chitikineni A, Visendi P, Gaur PM, Millan T, Singh KB, Taran B, Wang J, Batley J, Dolezel 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

39. Mason AS, Nelson MN, Takahira J, Cowling WA, Moreira Alves G, Chaudhuri A, Chen N, Ragu ME, Dalton-Morgan J, Coriton O, Huteau V, Eber F, Chevre A-M and Batley J. 2014. The Fate of Chromosomes and Alleles in an Allohexaploid Brassica Population. Genetics.197: 273-283

40. Mason AS, Batley J, Bayer PE, Hayward A, Cowling WA and Nelson MN. 2014. High resolution molecular karyotyping uncovers pairing between ancestrally related Brassica chromosomes. New Phytologist. 202: 964-974

41. Mirzaei S, Batley J, Ferguson B and Gresshoff PM. 2014 Transcriptome profiling of the shoot and root tips of S562L, a soybean GmCLAVATA1A mutant. Atlas Journal of Biology 3: 183-205.


2013

42. Visendi P, Batley J and Edwards D. 2013 Next generation characterisation of cereal genomes for marker discovery. Biology 2: 1357-1377

43. 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. In Press (accepted September 2013).

44. Golicz AA, Bayer PE, Martinez PA, Lai K, Lorenc MT, Alamery S, Hayward A, Tollenaere R, Long Y, Meng J, Batley J and Edwards D. 2013 Characterising diversity in the Brassica genomes. Acta Horticulturae .1005: 33-48

45. Zander M, Patel DA, Van de Wouw A, Lai K, Lorenc MT, Campbell E, Hayward A, Edwards D, Raman H and Batley J. 2013 Identifying genetic diversity of avirulence genes of Leptosphaeria maculans using whole genome sequencing. Functional and Integrative Genomics 13: 295-308

46. Berkman PJ, Visendi P, Lee HC, Stiller J, Manoli S, Lorenc MT, 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 11:564-571.

47. Raman H, Raman R, Kilian A, Detering F, Long Y, Edwards D, Parkin I, Sharpe A, Nelson M, Larkan N, Zou J, Meng J, Aslam M, Batley J, Cowling W and 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

48. Duran C, Singhania R, Raman H, Batley J and Edwards D. 2013 Predicting polymorphic EST-SSRs in silico. Molecular Ecology Resources 13: 538-545

49. Edwards D, Batley J and Snowden R. 2013 Accessing complex crop genomes with next-generation sequencing. Theoretical and Applied Genetics. 126:1-11

50. Raman H, Raman R, Eckermann P, Coombes N, Manoli S, Zhu X, Edwards D, Meng J, Prangnell R, Stiller J, Batley J, Luckett D, Wratten N and Dennis L. 2013 Genetic and physical mapping of flowering time loci in oilseed rape (Brassica napus L.). Theoretical and Applied Genetics 126: 119-132


2012

51. Kazakoff SH, Imelfort M, Edwards D, Koehorst J, Biswas B, Batley J, Scott P and Gresshoff PM. 2012. Capturing the biofuel wellhead and powerhouse: the chloroplast and mitochondrial genomes of the leguminous feedstock tree Pongamia pinnata. PLoS ONE 7: e51687

52. Lorenc MT, Hayashi S, Stiller J, Lee H, Manoli S, Ruperao P, Visendi P, Berkman PJ, Lai K, Batley J and Edwards D. 2012. Discovery of single nucleotide polymorphisms in complex genomes using SGSautoSNP. Biology 1: 370-382

53. 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 and Raman H. 2012. 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: 405-418

54. Hayward A, Mason A, Dalton Morgan J, Zander M, Edwards D and Batley J. 2012. SNP discovery and applications in Brassica napus. Journal of Plant Biotechnology 39: 1-12.

55. Lai K, Duran C, Berkman P, Lorenc M, Stiller J, Manoli S, Hayden M, Fleury D, Zander M, Mason A, Bauman U, Batley J and Edwards D. 2012. Single Nucleotide Polymorphism Discovery from Wheat Next Generation Sequence Data. Plant Biotechnology Journal 10:743-749

56. Hayward A, Vighnesh G, Delay C, Samian MR, Jiang Y, Manoli S, Stiller J, McKenzie M, Edwards D and Batley J. 2012. Next Generation Sequencing for Gene Homology Analysis in the Brassicaceae. Plant Biotechnology Journal. 10:750-759

57. Tollenaere R, Hayward A, Dalton-Morgan J, Campbell E, Lee JRM, 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 10:709-715

58. Berkman PJ, Skarshewski A, Manoli S, Lorenc MT, Stiller J, Smits L, Lai K, Campbell E, Simkova H, Batley J, Dolezel J, Hernandez P and Edwards D. 2012. Delimiting a translocation between wheat chromosome arms 7BS and 4AL with second generation sequencing. Theoretical and Applied Genetics 124:423-432

59. 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 14:1-10


2011

60. The Brassica rapa Genome Sequencing Project Consortium. 2011. The genome of the mesopolyploid crop species Brassica rapa. Nature Genetics 43:1035-1040

61. Berkman PJ, Skarshewski A, Lorenc MT, Lai K, Duran C, Ling EYS, Stiller J, Smits L, Imelfort M, Manoli S, McKenzie M, Kubalakova M, Simkova H, Batley J, Fleury D, Dolezel 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: 768-775.

62. Koo DH, Hong CP, Batley J, Chung YS, Edwards D, Bang JW, PhD; Hur Y and Lim YP. 2011. Rapid Divergence of Repetitive DNAs in Brassica Relatives. Genomics 97: 173-185

63. 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


2010

64. Mun J, Kwon S, Seol Y, Kim J, Jin M, Kim J, Lim M, Lee S, Hong J, Park T, Lee S, Kim B, Seo M, Baek S, Lee M, Shin J, Hahn J, Hwang Y, Lim K, Park J, Lee J, Yang T, Yu H, Choi I, Choi B, Choi S, Ramchiary N, Lim Y, Fraser F, Drou N, Soumpourou E, Trick M, Bancroft I, Sharpe AG, Parkin IA, Batley J, Edwards D and Park B. 2010. Sequence and structure of Brassica rapa chromosome A3. Genome Biology, 11:R94

65. 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.

66. 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: 273-274

67. Kaur S, Cogan NOI, 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 and Spangenberg GC. 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: 71-83

68. Edwards D and Batley J. 2010. Plant Genome Sequencing: Applications for Crop Improvement. Plant Biotechnology Journal 8: 2-9


2009 and earlier

69. Batley J and Edwards D. 2009. Genome sequence data: management, storage and visualization. Biotechniques 46: 333-336

70. 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: 326-333

71. Imelfort M, Duran C, Batley J and Edwards D. 2009. Discovering genetic polymorphisms in next generation sequencing data. Plant Biotechnology Journal. 7: 312-317

72. Duran C, Appleby N, Edwards D and Batley J. 2009. Molecular genetic markers: discovery, applications, data storage and visualisation. Current Bioinformatics 4: 16-27

73. 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

74. 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

75. 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 B-S and Lim YP. 2007. The reference genetic linkage map for the multinational Brassica rapa genome sequencing project. Theoretical and Applied Genetics 115:777-792

76. 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

77. Hong CP, Piao ZY, Kang TW, Batley J, Yang T-J, Hur Y-K, Bhak J, Edwards D and Lim YP. 2007. Genomic distribution of Simple Sequence Repeats in Brassica rapa. Mol. Cells 23: 349-356

78. 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

79. 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

80. 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

81. Iglesias-Rodrieguez MD, Probert I and Batley J. 2006. Microsatellite cross amplification in coccolithophores: application in population diversity studies. Hereditas 143: 99-102

82. 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

83. 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 84. Iglesias-Rodriguez MD, Schofield OM, Batley J, Medlin LK and Hayes PK. 2006. Extensive intraspecific genetic diversity in the marine coccolithophorid Emiliania huxleyi: the use of microsatellite analysis in marine phytoplankton population studies. Journal of Phycology 42: 526-536

85. 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

86. 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

87. 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 Hort. 706: 77-82

88. 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 Hort. 706: 115-119

89. 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

90. 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

91. 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

92. Edwards D and Batley J. 2004. Plant Bioinformatics: From Genome to Phenome. Trends in Biotechnology 22: 232-237

93. 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

94. 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

95. Batley J, Barker JHA, Dawson K, Edwards KJ, Wiltshire CW, Glen DM and Karp A. 2004. Microsatellite analysis of populations of the blue and brassy willow beetles, Phyllodecta vulgatissima and P. vitellinae, from UK willow plantations. Insect Molecular Biology 13: 413-421

96. Peacock L, Batley J, Dungait J, Barker JHA and Karp A. 2004. A comparative study of interspecies mating of Phratora vulgatissima and P. vitellinae using behavioural tests and molecular markers. Entomologia experimentalis et applicata 110: 231-241

97. Love CG, Batley J and Edwards D. 2003. Applied Computational Tools for Crop Genome Research. Journal of Plant Biotechnology 5: 193-195

98. 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

99. 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

100. Batley J and Hayes P. 2003. Development of high throughput single nuceltoide polymorphism genotyping for the analysis of Nodularia (Cyanobacteria) population genetics. Journal of Phycology 39: 248-252.

101. Tommasini L, Batley J, Arnold G, Cooke RG, Donini P, Lee D, Law J, Moule C, Trick M, and Edwards KJ. 2003. Application of fluorescence-based automated sizing of Multiplex Simple Sequence Repeats (SSR) marker sets for Testing Distinctness and Uniformity of Brassica napus L. Varieties. Theoretical and Applied Genetics 106: 1091-1101

102. 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

103. 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

104. Iglesias-Rodríguez D, Garcia Sáez A, Groben R, Edwards KJ, Batley J, Medlin LK, and Hayes PK. 2002. Polymorphic microsatellite loci in global populations of the marine coccolithophorid Emiliania huxleyi. Molecular Ecology Notes 2: 495-497

105. 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

106. Hayes PK, Barker GLA, Batley J, Beard SJ, Handley BA, Vacharapiyasophon P and Walsby AE. 2002. Genetic diversity within populations of cyanobacteria assessed by analysis of single filaments. Antonie van Leeuwenhoek 81: 197-202

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. Batley J, Edwards KJ, Wiltshire CW, Glen D and Karp A. 1998. The isolation and characterisation of microsatellite loci in the willow beetles Phyllodecta vulgatissima (L.) and P. vitellinae (L.). Mol Ecol 7: 1434-1436.