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2024 Journal Article The complex polyploid genome architecture of sugarcaneHealey, 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 |
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2024 Journal Article Factors affecting the germination of teliospores of Sporisorium scitamineum and the development of sugarcane smut in the fieldHidayah, 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 |
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2023 Journal Article Optimising clonal performance in sugarcane: leveraging non-additive effects via mate-allocation strategiesYadav, 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 |
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2022 Journal Article Combining genomic selection with genome-wide association analysis identified a large-effect QTL and improved selection for red rot resistance in sugarcaneO’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 |
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2022 Journal Article Isolation and sequencing of a single copy of an introgressed chromosome from a complex genome for gene and SNP identificationMetcalfe, 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 |
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2021 Journal Article Resistance mechanisms and expression of disease resistance-related genes in sugarcane (Sacchrum officinarum) to Sporisorium scitamineum infectionHidayah, 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 |
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2021 Journal Article Sugarcane smut, caused by Sporisorium scitamineum, a major disease of sugarcane: A contemporary reviewBhuiyan, 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 |
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2021 Journal Article A linkage disequilibrium-based approach to position unmapped SNPs in crop speciesYadav, 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 |
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2021 Journal Article Genomic selection in sugarcane: current status and future prospectsMahadevaiah, 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 |
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2021 Journal Article Strategies and considerations for implementing genomic selection to improve traits with additive and non-additive genetic architectures in sugarcane breedingVoss-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 |
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2021 Journal Article Accuracy of genomic prediction of complex traits in sugarcaneHayes, 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 |
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2020 Journal Article A perfect storm: ploidy and preadaptation facilitate Saccharum spontaneum escape and invasion in the Republic of PanamaSaltonstall, 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 |
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2020 Journal Article Accelerating genetic gain in sugarcane breeding using genomic selectionYadav, 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 |
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2019 Journal Article Flow cytometric characterisation of the complex polyploid genome of Saccharum officinarum and modern sugarcane cultivarsaMetcalfe, 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 |
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2018 Journal Article A mosaic monoploid reference sequence for the highly complex genome of sugarcaneGarsmeur, 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 |
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2018 Journal Article Analysis of the resistance mechanisms in sugarcane during Sporisorium scitamineum infection using RNA-seq and microscopyMcNeil, 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 |
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2018 Journal Article A high-resolution genetic map of the cereal crown rot pathogen Fusarium pseudograminearum provides a near-complete genome assemblyGardiner, 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 |
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2015 Journal Article DNA marker transmission and linkage analysis in populations derived from a sugarcane (Saccharum spp.) x Erianthus arundinaceus hybridChen, 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 |
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2015 Journal Article Complete genome sequence of Sporisorium scitamineum and biotrophic interaction transcriptome with sugarcaneTaniguti, 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 |
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2014 Journal Article Comparative mapping in the Poaceae family reveals translocations in the complex polyploid genome of sugarcaneAitken, 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 |
