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Agronomy 2017, 7(1), 14; doi:10.3390/agronomy7010014

Generation and Characterisation of a Reference Transcriptome for Phalaris (Phalaris aquatica L.)

Agriculture Victoria, AgriBio, the Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria 3083, Australia
CSIRO Agriculture Flagship, Canberra, Australian Capital Territory 2601, Australia
Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria 3010, Australia
School of Applied Systems Biology, La Trobe University, Bundoora, Victoria 3086, Australia
Author to whom correspondence should be addressed.
Academic Editor: Chengdao Li
Received: 24 October 2016 / Revised: 8 December 2016 / Accepted: 25 January 2017 / Published: 15 February 2017
(This article belongs to the Special Issue Application of Sequencing Technologies to Crop Breeding)
View Full-Text   |   Download PDF [1936 KB, uploaded 15 February 2017]   |  


Phalaris aquatica is a cool-season perennial grass species that is extensively cultivated in Australia, with additional usage in other areas of the world. Phalaris displays a number of desirable agronomic characteristics, although unfavourable traits include excessive seed shattering, sensitivity to aluminium toxicity, and several toxicosis syndromes. Varietal development has to date been based on traditional selection methods, but would benefit from the application of genomics-based approaches, which require the development of large-scale sequence resources. Due to a large nuclear DNA content, methods that target the expressed component of the genome and reduce the complexity of analysis are most amenable to current sequencing technologies. A reference unigene set has been developed by transcriptome sequencing of multiple tissues from a single plant belonging to the variety Landmaster. Comparisons have been made to gene complements from related species, as well as reference protein databases, and patterns of gene expression in different tissues have been evaluated. A number of candidate genes relevant to removal of undesirable attributes have been identified. The reference unigene set will provide the basis for detailed studies of differential gene expression and identification of candidate genes for potential transgenic deployment, as well as a critical resource for genotypic analysis to support future genomics-assisted breeding activities for phalaris improvement. View Full-Text
Keywords: RNA-Seq; harding grass; de novo assembly; sequence annotation; tissue-specific gene expression; P. tuberosa; Poaceae RNA-Seq; harding grass; de novo assembly; sequence annotation; tissue-specific gene expression; P. tuberosa; Poaceae

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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Baillie, R.C.; Drayton, M.C.; Pembleton, L.W.; Kaur, S.; Culvenor, R.A.; Smith, K.F.; Spangenberg, G.C.; Forster, J.W.; Cogan, N.O.I. Generation and Characterisation of a Reference Transcriptome for Phalaris (Phalaris aquatica L.). Agronomy 2017, 7, 14.

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