Dr Karen Aitken
Senior Principal Research Fellow
Queensland Alliance for Agriculture and Food Innovation
+61 7 344 38697
Book Chapters
Aitken, Karen and McNeil, Meredith (2010). Diversity analysis. Genetics, Genomics and Breeding of Sugarcane. (pp. 19-42) Boca Raton, FL United States: CRC Press. doi: 10.1201/EBK1578086849
Huang, Emma, Aitken, Karen and George, Andrew (2010). Association studies. Genetics, genomics and breeding of sugarcane. (pp. 43-68) Boca Raton, FL, United States: CRC Press. doi: 10.1201/EBK1578086849
Journal Articles
Healey, A. L., Garsmeur, O., Lovell, J. T., Shengquiang, S., Sreedasyam, A., Jenkins, J., Plott, C. B., Piperidis, N., Pompidor, N., Llaca, V., Metcalfe, C. J., Doležel, J., Cápal, P., Carlson, J. W., Hoarau, J. Y., Hervouet, C., Zini, C., Dievart, A., Lipzen, A., Williams, M., Boston, L. B., Webber, J., Keymanesh, K., Tejomurthula, S., Rajasekar, S., Suchecki, R., Furtado, A., May, G., Parakkal, P. ... D’Hont, A. (2024). The complex polyploid genome architecture of sugarcane. Nature, 628 (8009), 1-7. doi: 10.1038/s41586-024-07231-4
Hidayah, Nurul, Bhuiyan, Shamsul A., Aitken, Karen and Galea, Victor (2024). Factors affecting the germination of teliospores of Sporisorium scitamineum and the development of sugarcane smut in the field. Journal of Phytopathology, 172 (2) e13307, 1-10. doi: 10.1111/jph.13307
Yadav, Seema, Ross, Elizabeth M., Wei, Xianming, Powell, Owen, Hivert, Valentin, Hickey, Lee T., Atkin, Felicity, Deomano, Emily, Aitken, Karen S., Voss-Fels, Kai P. and Hayes, Ben J. (2023). Optimising clonal performance in sugarcane: leveraging non-additive effects via mate-allocation strategies. Frontiers in Plant Science, 14 1260517, 1260517. doi: 10.3389/fpls.2023.1260517
O’Connell, Anthony, Deo, Jasmin, Deomano, Emily, Wei, Xianming, Jackson, Phillip, Aitken, Karen S., Manimekalai, Ramaswamy, Mohanraj, Krishnasamy, Hemaprabha, Govinda, Ram, Bakshi, Viswanathan, Rasappa and Lakshmanan, Prakash (2022). Combining genomic selection with genome-wide association analysis identified a large-effect QTL and improved selection for red rot resistance in sugarcane. Frontiers in Plant Science, 13 1021182, 1-16. doi: 10.3389/fpls.2022.1021182
Metcalfe, Cushla J., Li, Jingchuan, Zheng, Bangyou, Stiller, Jiri, Healey, Adam, Piperidis, Nathalie and Aitken, Karen S. (2022). Isolation and sequencing of a single copy of an introgressed chromosome from a complex genome for gene and SNP identification. Theoretical and Applied Genetics, 135 (4), 1279-1292. doi: 10.1007/s00122-022-04030-1
Hidayah, Nurul, McNeil, Meredith, Li, Jingchuan, Bhuiyan, Shamsul, Galea, Victor and Aitken, Karen (2021). Resistance mechanisms and expression of disease resistance-related genes in sugarcane (Sacchrum officinarum) to Sporisorium scitamineum infection. Functional Plant Biology, 48 (12), 1302-1314. doi: 10.1071/FP21122
Bhuiyan, Shamsul A., Magarey, Robert C., McNeil, Meredith D. and Aitken, Karen S. (2021). Sugarcane smut, caused by Sporisorium scitamineum, a major disease of sugarcane: A contemporary review. Phytopathology, 111 (11), 1905-1917. doi: 10.1094/PHYTO-05-21-0221-RVW
Yadav, Seema, Ross, Elizabeth M., Aitken, Karen S., Hickey, Lee T., Powell, Owen, Wei, Xianming, Voss-Fels, Kai P. and Hayes, Ben J. (2021). A linkage disequilibrium-based approach to position unmapped SNPs in crop species. BMC Genomics, 22 (1) 773, 1-9. doi: 10.1186/s12864-021-08116-w
Mahadevaiah, Channappa, Appunu, Chinnaswamy, Aitken, Karen, Suresha, Giriyapura Shivalingamurthy, Vignesh, Palanisamy, Swamy, Huskur Kumaraswamy Mahadeva, Valarmathi, Ramanathan, Hemaprabha, Govind, Alagarasan, Ganesh and Ram, Bakshi (2021). Genomic selection in sugarcane: current status and future prospects. Frontiers in Plant Science, 12 708233, 1-18. doi: 10.3389/fpls.2021.708233
Hayes, Ben J., Wei, Xianming, Joyce, Priya, Atkin, Felicity, Deomano, Emily, Yue, Jenny, Nguyen, Loan, Ross, Elizabeth M., Cavallaro, Tony, Aitken, Karen S. and Voss-Fels, Kai P. (2021). Accuracy of genomic prediction of complex traits in sugarcane. Theoretical and Applied Genetics, 134 (5), 1455-1462. doi: 10.1007/s00122-021-03782-6
Voss-Fels, Kai P., Wei, Xianming, Ross, Elizabeth M., Frisch, Matthias, Aitken, Karen S., Cooper, Mark and Hayes, Ben J. (2021). Strategies and considerations for implementing genomic selection to improve traits with additive and non-additive genetic architectures in sugarcane breeding. Theoretical and Applied Genetics, 134 (5), 1493-1511. doi: 10.1007/s00122-021-03785-3
Saltonstall, Kristin, Bonnett, Graham D. and Aitken, Karen S. (2020). A perfect storm: ploidy and preadaptation facilitate Saccharum spontaneum escape and invasion in the Republic of Panama. Biological Invasions, 23 (4), 1101-1115. doi: 10.1007/s10530-020-02421-3
Yadav, Seema, Jackson, Phillip, Wei, Xianming, Ross, Elizabeth M., Aitken, Karen, Deomano, Emily, Atkin, Felicity, Hayes, Ben J. and Voss-Fels, Kai P. (2020). Accelerating genetic gain in sugarcane breeding using genomic selection. Agronomy, 10 (4) 585, 1-21. doi: 10.3390/agronomy10040585
Metcalfe, Cushla J., Li, Jingchuan, Giorgi, Debora, Dolezel, Jaroslav, Piperidis, Nathalie and Aitken, Karen S. (2019). Flow cytometric characterisation of the complex polyploid genome of Saccharum officinarum and modern sugarcane cultivarsa. Scientific Reports, 9 19362, 1-12. doi: 10.1038/s41598-019-55652-3
Garsmeur, Olivier, Droc, Gaetan, Antonise, Rudie, Grimwood, Jane, Potier, Bernard, Aitken, Karen, Jenkins, Jerry, Martin, Guillaume, Charron, Carine, Hervouet, Catherine, Costet, Laurent, Yahiaoui, Nabila, Healey, Adam, Sims, David, Cherukuri, Yesesri, Sreedasyam, Avinash, Kilian, Andrzej, Chan, Agnes, Van Sluys, Marie-Anne, Swaminathan, Kankshita, Town, Christopher, Bergès, Hélène, Simmons, Blake, Glaszmann, Jean Christophe, van der Vossen, Edwin, Henry, Robert, Schmutz, Jeremy and D'Hont, Angélique (2018). A mosaic monoploid reference sequence for the highly complex genome of sugarcane. Nature Communications, 9 (1) 2638, 1-10. doi: 10.1038/s41467-018-05051-5
McNeil, Meredith D., Bhuiyan, Shamsul A., Berkman, Paul J., Croft, Barry J. and Aitken, Karen S. (2018). Analysis of the resistance mechanisms in sugarcane during Sporisorium scitamineum infection using RNA-seq and microscopy. PLoS ONE, 13 (5) e0197840, 1-28. doi: 10.1371/journal.pone.0197840
Gardiner, Donald M., Benfield, Aurelie H., Stiller, Jiri, Stephen, Stuart, Aitken, Karen, Liu, Chunji and Kazan, Kemal (2018). A high-resolution genetic map of the cereal crown rot pathogen Fusarium pseudograminearum provides a near-complete genome assembly. Molecular Plant Pathology, 19 (1), 217-226. doi: 10.1111/mpp.12519
Chen, Jian-Wen, Lao, Fang-Ye, Chen, Xi-Wen, Deng, Hai-Hua, Liu, Rui, He, Hui-Yi, Fu, Cheng, Chen, Yong-Sheng, Liu, Fu-Ye, Li, Qi-Wei, Jackson, Phillip and Aitken, Karen (2015). DNA marker transmission and linkage analysis in populations derived from a sugarcane (Saccharum spp.) x Erianthus arundinaceus hybrid. PLoS ONE, 10 (6) e0128865. doi: 10.1371/journal.pone.0128865
Taniguti, Lucas M., Schaker, Patricia D. C., Benevenuto, Juliana, Peters, Leila P., Carvalho, Giselle, Palhares, Alessandra, Quecine, Maria C., Nunes, Filipe R. S., Kmit, Maria C. P., Wai, Alvan, Hausner, Georg, Aitken, Karen S., Berkman, Paul J., Fraser, James A., Moolhuijzen, Paula M., Coutinho, Luiz L., Creste, Silvana, Vieira, Maria L. C., Kitajima, João P. and Monteiro-Vitorello, Claudia B. (2015). Complete genome sequence of Sporisorium scitamineum and biotrophic interaction transcriptome with sugarcane. PLoS One, 10 (6) e0129318, e0129318. doi: 10.1371/journal.pone.0129318
Aitken, Karen S., McNeil, Meredith D., Berkman, Paul J., Hermann, Scott, Kilian, Andrzej, Bundock, Peter C. and Li, Jingchuan (2014). Comparative mapping in the Poaceae family reveals translocations in the complex polyploid genome of sugarcane. BMC Plant Biology, 14 (1) 190, 1-15. doi: 10.1186/s12870-014-0190-x
Berkman, Paul J., Bundock, Peter C., Casu, Rosanne E., Henry, Robert J., Rae, Anne L. and Aitken, Karen S. (2014). A Survey Sequence Comparison of Saccharum Genotypes Reveals Allelic Diversity Differences. Tropical Plant Biology, 7 (2), 71-83. doi: 10.1007/s12042-014-9139-3
Piperidis, N., Aitken, K. and Hermann, S. (2013). Towards a reliable method to select potentially high value Erianthus hybrids. International Sugar Journal, 115 (1379), 794-799.
Heller-Uszynska, Katarzyna, Uszynski, Grzegorz, Huttner, Eric, Evers, Margaret, Carlig, Jason, Caig, Vanessa, Aitken, Karen, Jackson, Phillip, Piperidis, George, Cox, Mike, Gilmour, Ross, D'Hont, Angelique, Butterfield, Mike, Glaszmann, Jean-Christophe and Kilian, Andrzej (2011). Diversity Arrays Technology effectively reveals DNA polymorphism in a large and complex genome of sugarcane. Molecular Breeding, 28 (1), 37-55. doi: 10.1007/s11032-010-9460-y
George, Andrew W. and Aitken, Karen (2010). A New Approach for Copy Number Estimation in Polyploids. Journal of Heredity, 101 (4), 521-524. doi: 10.1093/jhered/esq034
Baker, Peter, Jackson, Phillip and Aitken, Karen (2010). Bayesian estimation of marker dosage in sugarcane and other autopolyploids. Theoretical and Applied Genetics, 120 (8), 1653-1672. doi: 10.1007/s00122-010-1283-z
Liu, Xin-Long, Mao, Jun, Lu, Xin, Ma, Li, Aitken, Karen Sarah, Jackson, Phillip Andrew, Cai, Qing and Fan, Yuan-Hong (2010). Construction of molecular genetic linkage map of sugarcane based on SSR and AFLP markers: construction of molecular genetic linkage map of sugarcane based on SSR and AFLP markers. Zuowu Xuebao, 36 (1), 177-183. doi: 10.3724/sp.j.1006.2010.00177
Bundock, Peter C., Eliott, Frances G., Ablett, Gary, Benson, Adam D., Casu, Rosanne E., Aitken, Karen S. and Henry, Robert J. (2009). Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing. Plant Biotechnology Journal, 7 (4), 347-354. doi: 10.1111/j.1467-7652.2009.00401.x
Wang, Li-Ping, Jackson, Phillip A., Lu, Xin, Fan, Yuan-Hong, Foreman, John W., Chen, Xue-Kuan, Deng, Hai-Hua, Fu, Cheng, Ma, Li and Aitken, Karen S. (2008). Evaluation of sugarcane x Saccharum spontaneum progeny for biomass composition and yield components. Crop Science, 48 (3), 951-961. doi: 10.2135/cropsci2007.10.0555
Piperidis, Nathalie, Jackson, Phillip A., D'Hont, Angelique, Besse, Pascale, Hoarau, Jean-Yves, Courtois, Brigitte, Aitken, Karen S. and McIntyre, C. Lynne (2008). Comparative genetics in sugarcane enables structured map enhancement and validation of marker-trait associations. Molecular Breeding, 21 (2), 233-247. doi: 10.1007/s11032-007-9124-8
Aitken, K., Li, J., Wang, L., Qing, C., Fan, Y.H. and Jackson, P. (2007). Characterization of intergeneric hybrids of Erianthus rockii and Saccharum using molecular markers. Genetic Resources And Crop Evolution, 54 (7), 1395-1405. doi: 10.1007/s10722-006-9124-2
Mackie, J. M., Musial, J. M., Armour, D. J., Phan, H. T. T., Ellwood, S. E., Aitken, K. S. and Irwin, J. A. G. (2007). Identification of QTL for reaction to three races of Colletotrichum trifolii and further analysis of inheritance of resistance in autotetraploid lucerne. Theoretical and Applied Genetics, 114 (8), 1417-1426. doi: 10.1007/s00122-007-0527-z
Musial, J. M., Mackie, J. M., Armour, D. J., Phan, H. T. T., Ellwood, S. E., Aitken, K. S. and Irwin, J. A. G. (2007). Identification of QTL for resistance and susceptibility to Stagonospora meliloti in autotetraploid lucerne. Theoretical and Applied Genetics, 114 (8), 1427-1435. doi: 10.1007/s00122-007-0528-y
Wei, Xianming, Jackson, Phillip A., McIntyre, C. Lynne, Aitken, Karen S. and Croft, Barry (2006). Associations between DNA markers and resistance to diseases in sugarcane and effects of population substructure. Theoretical and Applied Genetics, 114 (1), 155-164. doi: 10.1007/s00122-006-0418-8
Aitken, K. S., Jackson, P. A. and McIntyre, C. L. (2006). Quantitative trait loci identified for sugar related traits in a sugarcane (Saccharum spp.) cultivar x Saccharum officinarum population. Theoretical and Applied Genetics, 112 (7), 1306-1317. doi: 10.1007/s00122-006-0233-2
Aitken, K. S., Li, J. C., Jackson, P., Piperidis, G. and McIntyre, C. L. (2006). AFLP analysis of genetic diversity within Saccharum officinarum and comparison with sugarcane cultivars. Australian Journal of Agricultural Research, 57 (11), 1167-1184. doi: 10.1071/AR05391
Cai, Q., Aitken, K. S., Fan, Y. H., Piperidis, G., Jackson, P. and McIntyre, C. L. (2005). A preliminary assessment of the genetic relationship between Erianthus rockii and the "saccharum complex" using microsatellite (SSR) and AFLP markers. Plant Science, 169 (5), 976-984. doi: 10.1016/j.plantsci.2005.07.002
Cai, Q., Aitken, K., Deng, H. H., Chen, X. W., Fu, C., Jackson, P. A. and McIntyre, C. L. (2005). Verification of the introgression of Erianthus arundinaceus germplasm into sugarcane using molecular markers. Plant Breeding, 124 (4), 322-328. doi: 10.1111/j.1439-0523.2005.01099.x
Reffay, N., Jackson, P. A., Aitken, K. S., Hoarau, J. Y., D'Hont, A., Besse, P. and McIntyre, C. L. (2005). Characterisation of genome regions incorporated from an important wild relative into Australian sugarcane. Molecular Breeding, 15 (4), 367-381. doi: 10.1007/s11032-004-7981-y
Aitken, K. S., Jackson, P. A. and McIntyre, C. L. (2005). A combination of AFLP and SSR markers provides extensive map coverage and identification of homo(eo)logous linkage groups in a sugarcane cultivar. Theoretical and Applied Genetics, 110 (5), 789-801. doi: 10.1007/s00122-004-1813-7
Shelton, D., Aitken, K., Doimo, L., Leach, D., Baverstock, P. and Henry, R. (2002). Genetic control of monoterpene composition in the essential oil of Melaleuca alternifolia (Cheel). Theoretical and Applied Genetics, 105 (2-3), 377-383. doi: 10.1007/s00122-002-0948-7
FRANCIS, DM, AITKEN, KS and STCLAIR, DA (1995). THE RELATIONSHIP BETWEEN MATING SYSTEM AND LYT ELEMENT ABUNDANCE IN LYCOPERSICON AND SOLANUM. Genetics, 140 (1), 418-419.
Conference Papers
Aitken, K. S., Giassop, D., Atkin, F. C., Parfitt, R. C., Drenth, J., Perroux, J. M. and Rae, A. L. (2019). How does stalk anatomy of sugarcane relate to fibre content and strength?. Annual Conference of the Australian-Society-of-Sugar-Cane-Technologists (ASSCT) / Congress of the International-Society-of-Sugar-Cane-Technologists - Plenary, Agricultural Engineering, Agronomy, Toowoomba, QLD Australia, 30 April-3 May 2019. Coulsdon, Surrey, United Kingdom: IHS Markit.
McNeil, Meredith D., Piperidis, George, Bhuiyan, Shamsul, Li, Jingchuan, Wei, Xianming, Collard, Bert and Aitken, Karen (2017). Development of a high-throughput, low-cost SNP genotyping panel for sugarcane breeding. 39th Conference of the Australian Society of Sugar Cane Technologists, ASSCT 2017, Cairns, QLD Australia, 3-5 May 2017. Mackay, QLD Australia: Australian Society of Sugar Cane Technologists.
Aitken, Karen, Berkman, Paul and Rae, Anne (2016). The first sugarcane genome assembly: how can we use it?. 38th Conference of the Australian Society of Sugar Cane Technologists (ASSCT 2016), Makay, QLD, Australia, 27 - 29 April 2016. Mackay, QLD, Australia: Australian Society of Sugar Cane Technologists.
Berkman, P. J., Casu, R. E., Stiller, J., Rae, A. L. and Aitken, K. S. (2015). Towards the sugarcane genome sequence and an understanding of polyploidy. 28th Congress of the International-Society-of-Sugar-Cane-Technologists, Sao Paulo Brazil, Jun 24-27, 2013. London: INT SUGAR JOURNAL LTD.
Glassop, D., Bonnett, G., Croft, B., Bhuiyan, S., Aitken, K. and Rae, A. (2014). Flowering-related genes are not involved in the development of smut whip. 36th Conference of the Australian Society of Sugar Cane Technologists, ASSCT 2014, Broadbeach, QLD Australia, 28 April - 1 May 2014. Mackay, QLD Australia: Australian Society of Sugar Cane Technologists.
Jackson, P. A., Fan, Y-H., Li, Q-W., Deng, H-H., Morgan, T. E., Piperidis, G. and Aitken, K. S. (2011). Utilisation of wild canes from China. 27th Congress of the International-Society-of-Sugar-Cane-Technologists, Veracruz Mexico, Mar 07-11, 2010. KENT: INT SUGAR JOURNAL LTD.
Whan, A. P., Robinson, N., Aitken, K. S., Lakshmanan, P. and Schmidt, S. (2008). Understanding nitrogen use efficiency in sugarcane: A quantitative genetics approach. 30th Annual Conference Australian Society of Sugar Cane Technologists, ASSCT 2008, Townsville, QLD, Australia, 29 April - 2 May 2008. Toowoomba, QLD Australia: Australian Society of Sugar Cane Technologists.
Fletcher, Andrew, Robinson, Nicole, Whan, Alex, Aitken, Karen, Critchley, Christa, Schmidt, Susanne and Laskhmanan, Prakash (2006). Reducing nitrogen input in sugarcane production: exploitation of genetic variability and specific nitrogen uptake characteristics holds the key. 28th Annual Conference of the Australian Society of Sugar Cane Technologists, ASSCT 2006, Mackay, QLD, Australia, 2-5 May 2006. Mackay, QLD, Australia: Australian Society of Sugar Cane Technologists.
Albertson, PL, Aitken, KS, Grof, CPL, Jackson, P, McIntyre, L, Piperidis, G and Berding, N (2001). Introgression of S-Officinarum -: A biochemical and molecular marker approach to improve CCS. 24th Congress of the International-Society-of-Sugar-Cane-Technologists, Brisbane Australia, Sep 17-21, 2001. MACKAY: AUSTRALIAN SOC SUGAR CANE TECHNOLOGISTS.
McIntyre, L, Aitken, K, Berding, N, Casu, R, Drenth, J, Jackson, P, Jordan, D, Piperidis, G, Reffay, N, Smith, G, Tao, YZ and Whan, (2001). Identification of DNA markers linked to agronomic traits in sugarcane in Australia. 24th Congress of the International-Society-of-Sugar-Cane-Technologists, Brisbane Australia, Sep 17-21, 2001. MACKAY: AUSTRALIAN SOC SUGAR CANE TECHNOLOGISTS.
Aitken, K, Botero, J, Zwart, R and Teasdale, R (1998). Detection of genetic diversity using RAPD markers in the genus Melaleuca. International Symposium on Biotechnology of Tropical and Subtropical Species, Brisbane Australia, Sep 29-Oct 03, 1997. LEUVEN 1: INTERNATIONAL SOCIETY HORTICULTURAL SCIENCE. doi: 10.17660/ActaHortic.1998.461.21
Preprint
Yadav, Seema, Ross, Elizabeth, Wei, Xianming, Powell, Owen, Hivert, Valentin, Hickey, Lee T., Atkin, Felicity, Deomano, Emily, Aitken, Karen S., Voss-Fels, Kai P. and Hayes, Ben J. (2022). Genomic mate-allocation strategies exploiting additive and non-additive genetic effects to maximise total clonal performance in sugarcane. doi: 10.1101/2022.12.19.521119