ARC QEII Research Fellow

Academic Achievement

2000: PhD, University of Bristol, Bristol, UK.
1996: MSc Ecology, University of Durham, UK
1995: BSc (Hons) Biology, University of Bristol, UK

Contact Details

School of Agriculture and Food Sciences and ARC Centre of Excellence for Integrative Legume Research
CILR, Level 2, John Hines Building
The University of Queensland
Brisbane 4072
Australia
Email: j.batley@uq.edu.au
Phone: +61 (0)7 334 69534
Mobile: 0423 841669
Batley Lab

Occupational Experience

05/2009 - current: ARC QEII Research Fellow, School of Land, Crop and Food Sciences, University of Queensland
03/2007 – 04/2009: Research Fellow, School of Land, Crop and Food Sciences, University of Queensland
08/2002 – 03/2007: Senior Research Scientist, Primary Industries Research Victoria, La Trobe University, Victoria and Technical Manager, AgGenomics Pty Ltd.
02/2001 - 07/2002: Postdoctoral Researcher, School of Biological Sciences, University of Bristol, UK.
10/2000 - 01/2001: Postdoctoral Researcher, IACR-Long Ashton Research Station, Bristol, UK.
01/2000 - 09/2000: Postdoctoral Researcher, Advanta Seeds UK, seconded to IACR-Long Ashton Research Station, Bristol, UK.
 

10/1999 - 12/1999: Postdoctoral Researcher, IACR-Long Ashton Research Station, Bristol, UK.

Awards and Prizes

In 2007, she was awarded the Chinese-Australia Young Scientist Exchange Scheme, which involved a visit to China to meet with the funding bodies and scientists to establish links and develop collaborations. This project led to successful collaborations as evidenced by the Australia-China International Science Linkage grants awarded in 2009. In 2010, she was invited back to China as an alumni of the Australia-china young scientist exchange scheme, and this has now led to her being awarded the “next step program – making collaboration happen”. In October 2008, she was awarded an ARC QEII fellowship for commencement in 2009 to investigate the co-evolution of host-pathogen interaction between blackleg and Brassica. In 2009 she received a University of Queensland Foundation Research Excellence Award, which recognises outstanding performance and leadership potential in early career researchers. This award also provided $70,000 to identify novel disease resistance genes in wild Brassicaceae.

Research Interests

Areas of interest include genetic and genomics analysis and specifically, genome sequence analysis and the development of molecular genetic marker systems for applications such as genetic diversity, genetic mapping, LD and comparative genomic studies and the molecular characterisation of agronomic traits. She is currently also focussing on blackleg resistance in Brassicas.

Current Competitive Grant Funding

• 2009: J Batley. Investigating the evolution and conservation of nodulation and mycorrhization genes across the Brassicaceae. University of Queensland Early Career Researcher Grant $27,000.

• 2009-2014: J Batley, D Edwards & R Delourme. Co-evolution of the host pathogen interaction between Leptosphaeria maculans and Brassica species. ARC Discovery $880,000

• 2009-2012: J Batley & D Edwards. Characterising genetic variation in Brassica napus. ARC Linkage in Partnership with NSWDPI, Bayer Crop Science (Belgium) and the Australian Genome Research Facility. $848,000 from the ARC and $456,000 partner cash contribution

• 2009-2011: J Batley, D Edwards & N Nesi. Characterisation of candidate genes underlying oil quality in Canola (Brassica napus) French-Australia Science and Technology programme (FR090077) $14,000

• 2009-2014: D Edwards, H Raman & J Batley. Development of molecular markers for application in Australian canola breeding. GRDC $2.5 m

• 2010: J Batley. Conservation of blackleg disease resistance genes across the Brassicaceae: an insight into the Brassicaceae evolution. University of Queensland Foundation Research Excellence Award $70,000.

• 2010-2011: J Batley & D Edwards. Applying the Brassica rapa genome sequence to identify candidate genes underlying agronomic traits in canola (Brassica napus). DEST Australia-China International Science Linkage $49,000

• 2010-2011: D Edwards & J Batley. Sequencing and annotating the C Genome of Brassica. DEST Australia-China International Science Linkage $96,500

• 2011: J Batley, D Edwards, M Nelson & W Cowling. Second Generation sequencing to identify genes controlling flowering in oilseed Brassica plants. UQ-UWA Bilateral Research Collaboration Award $20,000

• 2011-2013: D Edwards & J Batley. Mapping recombination blocks in Brassica. ARC Linkage in Partnership with Bayer Crop Science (Belgium). $611,000 from the ARC and $500,000 partner cash contribution.

Past Competitive Grant Funding

• 2008-2009: J Batley. Characterising genetic variation in sorghum. UQ FirstLink Funding $3,000

• 2006-2007: D Edwards & J Batley. Establishing shared resources for the identification of Blackleg disease resistance genes in canola (Brassica napus). French-Australia Science and Technology programme. $16,000.

Publications

Books:

1. Oilseed Brassicas Eds. Edwards D, Batley J and Parkin I. Science Publishers Inc (USA) (In press, accepted December 2010)

Book Chapters:

1. Hayward A (2010) Introduction - Oilseed Brassicas. In: Oilseed Brassicas (Eds Edwards D, Batley J and Parkin I) Science Publishers Inc (USA) (In press, accepted December 2010)
2. 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
3. Duran C, Boskovic Z, Batley J and Edwards D. Brassica Bioinformatics. In: Vegetable Brassicas (Ed. Sadowski J) Science Publishers Inc (USA) (In press, accepted March 2009)
4. 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
5. 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
6. 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
7. 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
8. 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
9. 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
10. 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
11. 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
12. 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
13. 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
14. 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
15. 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
16. 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
17. 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:

1. Hayward A, McLanders J, Campbell E, Edwards D and Batley J. 2011. Genomic advances will herald new insights into the Brassica:Leptosphaeria maculans pathosystem. Plant Biology (In Press: accepted March 2011)
2. 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 (In press: accepted December 2010).
3. 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
4. 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
5. 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
6. 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.
7. 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
8. 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
9. Edwards D and Batley J. 2010. Plant Genome Sequencing: Applications for Crop Improvement. Plant Biotechnology Journal 8: 2-9
10. Batley J and Edwards D. 2009. Genome sequence data: management, storage and visualization. Biotechniques 46: 333-336
11. 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
12. Imelfort M, Duran C, Batley J and Edwards D. 2009. Discovering genetic polymorphisms in next generation sequencing data. Plant Biotechnology Journal. 7: 312-317
13. Duran C, Appleby N, Edwards D and Batley J. 2009. Molecular genetic markers: discovery, applications, data storage and visualisation. Current Bioinformatics 4: 16-27
14. 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
15. 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
16. 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
17. 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
18. 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
19. 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
20. 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
21. 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
22. Iglesias-Rodrieguez MD, Probert I and Batley J. 2006. Microsatellite cross amplification in coccolithophores: application in population diversity studies. Hereditas 143: 99-102
23. 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
24. 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
25. 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
26. 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
27. 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
28. 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
29. 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
30. 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
31. 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
32. 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
33. Edwards D and Batley J. 2004. Plant Bioinformatics: From Genome to Phenome. Trends in Biotechnology 22: 232-237
34. 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
35. 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
36. 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
37. 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
38. Love CG, Batley J and Edwards D. 2003. Applied Computational Tools for Crop Genome Research. Journal of Plant Biotechnology 5: 193-195
39. 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
40. 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
41. 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.
42. 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
43. 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
44. 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
45. 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
46. 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
47. 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
48. 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
49. 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.

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