Dr Alison Kelly
Senior Research Fellow in Statistic
Centre for Crop Science
Adjunct Associate Professor
Centre for Nutrition & Food Sciences (QAAFI)
Book Chapters
Kelly, Alison and Forknall, Clayton (2020). Advanced designs for barley breeding experiments. Achieving sustainable cultivation of barley. (pp. 159-181) edited by Glen Fox and Chengdao Li. Cambridge, United Kingdom: Burleigh Dodds Science Publishing. doi: 10.19103/as.2019.0060.06
Kelly, A. M. and Basford, K. E. (2000). Pattern analysis in grassland and animal production systems. Field and Laboratory Methods for Grassland and Animal Production Research. (pp. 9-28) edited by L. 't Mannetje and R. M. Jones. Wallingford: CABI Publishing.
Journal Articles
Bottomley, Prue, Sutherland, Mark W., Wilson, Bree A.L., Rognoni, Bethany, Kelly, Alison and Percy, Cassandra D. (2024). Soil solarisation delivers near zero levels of Fusarium pseudograminearum in cereal crown rot reference sites. Crop Protection, 185 106887, 106887. doi: 10.1016/j.cropro.2024.106887
Rognoni, Bethany, Forknall, Clayton R., Simpfendorfer, Steven, Daniel, Richard, Neale, Luke and Kelly, Alison M. (2024). Quantifying the resistance of Australian wheat genotypes to Pratylenchus thornei based on a continuous metric from a factor analytic linear mixed model. Euphytica, 220 (9) 141. doi: 10.1007/s10681-024-03387-2
Keno, Tolera, Mace, Emma, Godwin, Ian, Jordan, David and Kelly, Alison (2024). The use of fixed shelling percentage biases genotype selection in hybrid maize multi-environment yield trials. Field Crops Research, 315 109437, 1-9. doi: 10.1016/j.fcr.2024.109437
Abdulsada, Rian R., Thompson, Michael, Peitton, Lucas, Kelly, Alison and Percy, Cassandra D. (2024). Fusarium pseudograminearum infected wheat lines vary in disease severity and gas exchange response under different watering regimes. Plant Pathology, 73 (3), 602-612. doi: 10.1111/ppa.13843
Mumford, Michael H., Forknall, Clayton R., Rodriguez, Daniel, Eyre, Joseph X. and Kelly, Alison M. (2023). Incorporating environmental covariates to explore genotype × environment × management (G × E × M) interactions: A one-stage predictive model. Field Crops Research, 304 109133, 1-15. doi: 10.1016/j.fcr.2023.109133
Forknall, Clayton R., Verbyla, Arūnas P., Nazarathy, Yoni, Yousif, Adel, Osama, Sarah, Jones, Shirley H., Kerr, Edward, Schulz, Benjamin L., Fox, Glen P. and Kelly, Alison M. (2023). Covariance clustering: modelling covariance in designed experiments when the number of variables is greater than experimental units. Journal of Agricultural, Biological and Environmental Statistics, 29 (2), 232-256. doi: 10.1007/s13253-023-00574-x
Borrell, Andrew K., Christopher, John T., Kelly, Alison, Collins, Brian and Chenu, Karine (2023). Balancing pre- and post-anthesis growth to maximise water-limited yield in cereals. Field Crops Research, 296 108919, 1-19. doi: 10.1016/j.fcr.2023.108919
Coast, Onoriode, Posch, Bradley C., Rognoni, Bethany G., Bramley, Helen, Gaju, Oorbessy, Mackenzie, John, Pickles, Claire, Kelly, Alison M., Lu, Meiqin, Ruan, Yong‐Ling, Trethowan, Richard and Atkin, Owen K. (2022). Wheat photosystem
II
heat tolerance: evidence for genotype‐by‐environment interactions. The Plant Journal, 111 (5), 1368-1382. doi: 10.1111/tpj.15894
Zheng, Zhi, Powell, Jonathan, Gao, Shang, Percy, Cassandra, Kelly, Alison, Macdonald, Bethany, Zhou, Meixue, Davies, Philip and Liu, Chunji (2022). Investigation of two QTL conferring seedling resistance to Fusarium crown rot in barley on reducing grain yield loss under field environments. Agronomy, 12 (6) 1282, 1282. doi: 10.3390/agronomy12061282
Paccapelo, M. Valeria, Kelly, Alison M., Christopher, Jack T. and Verbyla, Arūnas P. (2022). WGNAM: whole-genome nested association mapping. Theoretical and Applied Genetics, 135 (7), 2213-2232. doi: 10.1007/s00122-022-04107-x
Christopher, Mandy, Paccapelo, Valeria, Kelly, Alison, Macdonald, Bethany, Hickey, Lee, Richard, Cécile, Verbyla, Ari, Chenu, Karine, Borrell, Andrew, Amin, Asad and Christopher, Jack (2021). QTL identified for stay-green in a multi-reference nested association mapping population of wheat exhibit context dependent expression and parent-specific alleles. Field Crops Research, 270 108181, 108181. doi: 10.1016/j.fcr.2021.108181
Kelly, Alison, Macdonald, Bethany, Percy, Cassandra and Davies, Philip (2021). An improved method for selection of wheat genotypes for tolerance to crown rot caused by Fusarium pseudograminearum. Journal of Phytopathology, 169 (6), 339-349. doi: 10.1111/jph.12970
Osama, Sarah K., Kerr, Edward D., Yousif, Adel M., Phung, Toan K., Kelly, Alison M., Fox, Glen P. and Schulz, Benjamin L. (2021). Proteomics reveals commitment to germination in barley seeds is marked by loss of stress response proteins and mobilisation of nutrient reservoirs. Journal of Proteomics, 242 104221, 104221. doi: 10.1016/j.jprot.2021.104221
Reeves, Karyn L., Forknall, Clayton R., Kelly, Alison M., Owen, Kirsty J., Fanning, Joshua, Hollaway, Grant J. and Loughman, Robert (2020). A novel approach to the design and analysis of field experiments to study variation in the tolerance and resistance of cultivars to root lesion nematodes (Pratylenchus spp.). Phytopathology, 110 (10), 1623-1631. doi: 10.1094/phyto-03-20-0077-r
Forknall, Clayton R., Simpfendorfer, Steven and Kelly, Alison M. (2019). Using yield response curves to measure variation in the tolerance and resistance of wheat cultivars to Fusarium crown rot. Phytopathology, 109 (6), 932-941. doi: 10.1094/phyto-09-18-0354-r
Robinson, Hannah, Kelly, Alison, Fox, Glen, Franckowiak, Jerome, Borrell, Andrew and Hickey, Lee (2018). Root architectural traits and yield: exploring the relationship in barley breeding trials. Euphytica, 214 (9) 151. doi: 10.1007/s10681-018-2219-y
Nielsen, Sharon, Russell, Kenneth G., Kelly, Alison and Fox, Glen (2018). A data-driven near infrared calibration process including near infrared spectral thumbprints. Journal of Near Infrared Spectroscopy, 26 (3), 169-185. doi: 10.1177/0967033518782765
Voss-Fels, Kai P., Robinson, Hannah, Mudge, Stephen R., Richard, Cecile, Newman, Saul, Wittkop, Benjamin, Stahl, Andreas, Friedt, Wolfgang, Frisch, Matthias, Gabur, Iulian, Miller-Cooper, Anika, Campbell, Bradley C., Kelly, Alison, Fox, Glen, Christopher, Jack, Christopher, Mandy, Chenu, Karine, Franckowiak, Jerome, Mace, Emma S., Borrell, Andrew K., Eagles, Howard, Jordan, David R., Botella, Jose R., Hammer, Graeme, Godwin, Ian D., Trevaskis, Ben, Snowdon, Rod J. and Hickey, Lee T. (2017). VERNALIZATION1 modulates root system architecture in wheat and barley. Molecular Plant, 11 (1), 226-229. doi: 10.1016/j.molp.2017.10.005
Robinson, Hannah, Hickey, Lee, Richard, Cecile, Mace, Emma, Kelly, Alison, Borrell, Andrew, Franckowiak, Jerome and Fox, Glen (2016). Genomic regions influencing seminal root traits in barley. The Plant Genome, 9 (1), 1-13. doi: 10.3835/plantgenome2015.03.0012
Betts, Natalie S., Fox, Glen P., Kelly, Alison M., Cruickshank, Alan W., Lahnstein, Jelle, Henderson, Marilyn, Jordan, David R. and Burton, Rachel A. (2015). Non-cellulosic cell wall polysaccharides are subject to genotype times environment effects in sorghum (Sorghum bicolor) grain. Journal of Cereal Science, 63, 64-71. doi: 10.1016/j.jcs.2015.02.007
Sheedy, J. G., McKay, A. C., Lewis, J., Vanstone, V. A., Fletcher, S., Kelly, A. and Thompson, J. P. (2015). Cereal cultivars can be ranked consistently for resistance to root-lesion nematodes (Pratylenchus thornei & P. neglectus) using diverse procedures. Australasian Plant Pathology, 44 (2), 175-182. doi: 10.1007/s13313-014-0333-4
Martin, A., Bovill, W. D., Percy, C. D., Herde, D., Fletcher, S., Kelly, A., Neate, S. M. and Sutherland, M. W. (2015). Markers for seedling and adult plant crown rot resistance in four partially resistant bread wheat sources. Theoretical and Applied Genetics, 128 (3), 377-385. doi: 10.1007/s00122-014-2437-1
Silcock, R. G., Hall, T. J., Filet, P. G., Kelly, A. M., Osten, D. and Graham, T. W. G. (2015). Floristic composition and pasture condition of Aristida/Bothriochloa pastures in central Queensland. II. Soil and pasture condition interactions. Rangeland Journal, 37 (2), 217-226. doi: 10.1071/rj14107
Silcock, R. G., Hall, T. J., Filet, P. G., Kelly, A. M., Osten, D., Schefe, C. M. and Knights, P. T. (2015). Floristic composition and pasture condition of Aristida/Bothriochloa pastures in central Queensland. I. Pasture floristics. Rangeland Journal, 37 (2), 199-215. doi: 10.1071/rj14106
Fox, G. P., Martin, A., Kelly, A. M., Sutherland, M. W., Martin, D., Banks, P. M. and Sheppard, J. (2013). QTLs for water absorption and flour yield identified in a double haplod wheat population Lang/QT8766. Euphytica, 192 (3), 453-462. doi: 10.1007/s10681-013-0885-3
Peake, Allan S., Huth, Neil I., Kelly, Alison M. and Bell, Kerry L. (2013). Variation in water extraction with maize plant density and its impact on model application. Field Crops Research, 146, 31-37. doi: 10.1016/j.fcr.2013.02.012
Gous, Peter W., Martin, Anke, Lawson, Wendy, Kelly, Alison, Fox, Glen P. and Sutherland, Mark W. (2012). Correlation between NIRS generated and chemically measured feed quality data in barley (Hordeum vulgare), and potential use in QTL analysis identification. Euphytica, 188 (3), 325-332. doi: 10.1007/s10681-012-0644-x
Gous, Peter W., Martin, Anke, Lawson, Wendy, Kelly, Alison, Fox, Glen P. and Sutherland, Mark W. (2012). QTL associated with barley (Hordeum vulgare) feed quality traits measured through in situ digestion. Euphytica, 185 (1), 37-45. doi: 10.1007/s10681-011-0608-6
Sheedy, J. G., Thompson, J. P. and Kelly, A. (2012). Diploid and tetraploid progenitors of wheat are valuable sources of resistance to the root lesion nematode Pratylenchus thornei. Euphytica, 186 (2), 377-391. doi: 10.1007/s10681-011-0617-5
Fox, G. P., Kelly, A., Sweeney, N. and Hocorft, D. M. (2011). Development of a single kernel NIR barley protein calibration and assessment of variation in protein on grain quality. Journal of the Institute of Brewing, 117 (4), 582-586. doi: 10.1002/j.2050-0416.2011.tb00507.x
Thompson, John P., Reen, Roslyn A., Clewett, Timothy G., Sheedy, Jason G., Kelly, Alison M., Gogel, Beverley J. and Knights, Edward J. (2011). Hybridisation of Australian chickpea cultivars with wild Cicer spp. increases resistance to root-lesion nematodes (Pratylenchus thornei and P. neglectus). Australasian Plant Pathology, 40 (6), 601-611. doi: 10.1007/s13313-011-0089-z
Lawson, W., Mace, E., Collard, B. C. Y., Fox, G., Kelly, A., Sutherland, M., Franckowiak, J. and Bowman, J. (2010). QTL analysis of feed quality traits in two barley F6-derived RIL populations. SABRAO Journal of Breeding and Genetics.
Mann, Gulay, Diffey, Simon, Cullis, Brian, Azanza, Fermin, Martin, David, Kelly, Alison, McIntyre, Lynne, Schmidt, Adele, Ma, Wujun, Nath, Zena, Kutty, Ibrahim, Leyne, P. Emmett, Rampling, Lynette, Quail, Ken J. and Morell, Matthew K. (2009). Genetic control of wheat quality: interactions between chromosomal regions determining protein content and composition, dough rheology, and sponge and dough baking properties. Theoretical and Applied Genetics, 118 (8), 1519-1537. doi: 10.1007/s00122-009-1000-y
Kelly, Alison M., Cullis, Brian R., Gilmour, Arthur R., Eccleston, John A. and Thompson, Robin (2009). Estimation in a multiplicative mixed model involving a genetic relationship matrix. Genetics Selection Evolution, 41 (33) 33, 1-9. doi: 10.1186/1297-9686-41-33
Fox, G., Kelly, A., Bowman, J., Inkerman, A., Poulsen, D. and Henry, R. (2009). Is malting barley better feed for cattle than feed barley?. Journal of the Institute of Brewing, 115 (2), 95-104. doi: 10.1002/j.2050-0416.2009.tb00352.x
Fox, Glen P., Bowman, Jan, Kelly, Alison, Inkerman, Andy, Poulsen, David and Henry, Robert (2008). Assessing for genetic and environmental effects on ruminant feed quality in barley (Hordeum vulgare). Euphytica, 163 (2), 249-257. doi: 10.1007/s10681-007-9638-5
Fox, Glen P., Osborne, Brian, Bowman, Jan, Kelly, Alison, Cakir, Mehmet, Poulsen, David, Inkerman, Andy and Henry, Robert (2007). Measurement of genetic and environmental variation in barley (Hordeum vulgare) grain hardness. Journal of Cereal Science, 46 (1), 82-92. doi: 10.1016/j.jcs.2006.12.003
Osborne, B. G., Fox, G. P., Kelly, A. M. and Henry, R. J. (2007). Measurement of barley grain rheology for the quality selection of breeding material. Journal of the Institute of Brewing, 113 (2), 135-141. doi: 10.1002/j.2050-0416.2007.tb00269.x
Kelly, A. M., Smith, A. B., Eccleston, J. A. and Cullis, B. R. (2007). The accuracy of varietal selection using factor analytic models for multi-environment plant breeding trials. Crop Science, 47 (3), 1063-1070. doi: 10.2135/cropsci2006.08.0540
Fox, Glen P., Kelly, Alison, Poulsen, David, Inkerman, Andy and Henry, Robert (2006). Selecting for increased barley grain size. Journal of Cereal Science, 43 (2), 198-208. doi: 10.1016/j.jcs.2005.08.004
Fox, G. P., Kelly, A. M., Cakir, M., Bloustein, G., Poulsen, D. M. E., Inkerman, P. A. and Henry, R. J. (2006). Genetic impacts of the hull on barley grain quality. Journal of the Institute of Brewing, 112 (2), 101-107. doi: 10.1002/j.2050-0416.2006.tb00238.x
Lever, T., Kelly, A., De Faveri, J., Martin, D., Sheppard, J., Quail, K. and Miskelly, D. (2005). Australian wheat for the sponge and dough bread making process. Australian Journal of Agricultural Research, 56 (10), 1049-1057. doi: 10.1071/ar05113
Cruickshank, A.W., Tonks, J.W. and Kelly, A.K. (2003). Blanchability of peanut (Arachis hypogaea L.) kernels: early generation selection and genotype stability over three environments. Australian Journal of Agricultural Research, 54 (9), 885-888. doi: 10.1071/ar02126
Redden, R., Desborough, P., Tompkins, W., Usher, T. and Kelly, A. (2001). Responses of adzuki bean as affected by row spacing, plant density and variety. Australian Journal of Experimental Agriculture, 41 (2), 235-243. doi: 10.1071/ea00069
Tao, Y.Z., Henzell, R.G., Jordan, D.R., Butler, D.G., Kelly, A.M. and McIntyre, C.L. (2000). Identification of genomic regions associated with stay green in sorghum by testing RILs in multiple environments. Theoretical and Applied Genetics, 100 (8), 1225-1232. doi: 10.1007/s001220051428
Wildermuth, G.B., Thomas, G.A., Radford, B.J., McNamara, R.B. and Kelly, A. (1997). Crown rot and common root rot in wheat grown under different tillage and stubble treatments in southern Queensland, Australia. Soil & Tillage Research, 44 (3-4), 211-224. doi: 10.1016/s0167-1987(97)00054-8
Mitchell, J. and Kelly, A. (1992). Evaluating odour attractants for control of wild dogs. Wildlife Research, 19 (2), 211-219. doi: 10.1071/wr9920211
Cavaye, J.M. , Knight, J.L. , Tierney, T.J. and Kelly, A.M. (1992). Growth and carcass characteristics of three-way Africander multiply Simmental multiply Hereford crossbreds in south-western Queensland. Australian Journal of Experimental Agriculture, 32 (6), 675-681. doi: 10.1071/ea9920675
Mayer, D.G. , Schoorl, D. , Butler, D.G. and Kelly, A.M. (1991). Efficiency and fractal behaviour of optimisation methods on multiple-optima surfaces. Agricultural Systems, 36 (3), 315-328. doi: 10.1016/0308-521x(91)90013-z
Conference Papers
Fletcher, Andrew, Christopher, Jack, Kelly, Alison and Chenu, Karine (2022). Genomic prediction to accelerate breeding potential for increased transpiration efficiency in wheat. Australian Agronomy Conference, Toowoomba, QLD, Australia, 18-22 September 2022.
Borrell, Andrew, Christopher, Jack, Kelly, Alison, Collins, Brian and Chenu, Karine (2022). Maximising water-limited yield in cereals by balancing pre- and post-anthesis growth. Australian Agronomy Conference, Toowoomba, QLD, Australia, 18-22 September 2022.
Fletcher, Andrew, Kelly, Alison, Christopher, Jack, Paccapela, Valeria and Chenu, Karine (2019). Using high-throughput phenotyping and genome wide association study (GWAS) techniques to identify molecular markers for transpiration efficiency in wheat. Australian Agronomy Conference, Wagga Wagga, NSW Australia, 25-29 August 2019. Wagga Wagga, NSW, Australia: Australian Society of Agronomy.
Chenu, Karine, Fletcher, Andrew, Ababaei, Behnam, Christopher, Jack, Kelly, Alison, Hickey, Lee, Van Oosterom, Erik and Hammer, Graeme (2019). Integrating crop modelling, physiology, genetics and breeding to aid crop improvement for changing environments in the Australian wheatbelt. International Tropical Agriculture Conference (TROPAG 2019), Brisbane, Australia, 11–13 November 2019. Basel, Switzerland: MDPI AG. doi: 10.3390/proceedings2019036004
Chenu, Karine, Fletcher, Andrew, Ababaei, Behnam, Christopher, Jack, Kelly, A., Hickey, Lee, Van Oosterom, Erik and Hammer, Graeme (2019). Integrating crop modelling, physiology, genetics and breeding to aid crop improvement for changing environments. International Tropical Agriculture Conference (TropAg2019), Brisbane, QLD Australia, 11-13 November 2019.
Fletcher, A., Christopher, J., Kelly, A., Paccapelo, V. and Chenu, K. (2018). Genetics of transpiration efficiency in a wheat Nested Association Mapping population. 15th Plant Biology Europe, Copenhagen, Denmark, 18-21 June 2018.
Topp, B., Hardner, C. M., Neal, J., Kelly, A., Russell, D., McConchie, C. and O'Hare, P. (2016). Overview of the Australian macadamia industry breeding program. XXIX International Horticultural Congress on Horticulture: Sustaining Lives, Livelihoods and Landscapes (IHC2014), Brisbane, Australia, 17 - 22 August 2014. Leuven, Belgium: International Society for Horticultural Science. doi: 10.17660/ActaHortic.2016.1127.8
Neal, J. M., Kelly, A., Hardner, C. M., McConchie, C. and Topp, B. L. (2016). Preliminary evaluation of macadamia rootstocks for yield and tree height. 29th International Horticultural Congress on Horticulture - Sustaining Lives, Livelihoods and Landscapes (IHC) / International Symposium on Nut Crops, Brisbane Australia, Aug 17, 2014. Leuven, Belgium: International Society for Horticultural Science. doi: 10.17660/ActaHortic.2016.1109.30
Topp, B. L., Hardner, C. M. and Kelly, A. M. (2012). Strategies for breeding macadamias in Australia. IHC2010: 28th International Horticultural Congress on Science and Horticulture for People, Lisboa, Portugal, 22-27 August, 2010. Leuven, Belgium: International Society for Horticultural Science. doi: 10.17660/ActaHortic.2012.935.6
Franckowiak, J., Platz, G., Lawson, W., Killian, A, Fox, G., Kelly, A., Mace, E. and Jordan, D. (2011). Management of traits and genes involved in adaptation of barley to north-eastern Australia. 16th Australian Barley Technical Symposium, Adelaide, Australia, 18-21 September 2011.
Kelly, A., Fox, G., Franckowiak, J., Sweeney, N. and Only-Watson, K. (2011). Reverse Spectroscopy: bypassing the need for NIR calibration in a barley breeding program. 15th International Conference on Near Infrared Spectroscopy, Cape Town, South Africa, 13-20 May 2011.
Taylor, T., Kelly, A., Newberry, M., Cavangh, C., Martin, D. and Fox, G. (2011). Sponge & dough quality testing using RVA. 61st Australian Cereal Chemistry Conference, Coolongatta, NSW, Australia, 4-8 September 2011.
Lawson, W., Mace, E., Collard, B., Fox, G., Kelly, A., Sutherland, M. and Franckowiak, J. (2010). Investigating the molecular genetics of malt and feed quality traits in barley. 6th Canadian Barley Technical Symposium, Saskatoon, Saskatchewan, Canada, 25-28 July 2010. Saskatoon, Saskatchewan, Canada: University of Saskatchewan.
Thesis
Kelly, Alison Maree (2013). Estimation of a linear mixed model with a reduced rank variance matrix. PhD Thesis, School of Mathematics and Physics, The University of Queensland.