Perennial ryegrass (Lolium perenne L.) is a major grass species of temperate pastoral agriculture

Edwards, D.

Erwin, T. A.

Logan, E. G.

Love, C. G.

Ong, E. K.

Sawbridge, T.

Spangenberg, G. C.

English

University of Kentucky

University of Kentucky UKnowledge International Grassland Congress Proceedings XX International Grassland Congress Ryegrass ASTRA: a Web-Based Resource for Lolium EST Analysis G. C. Spangenberg La Trobe University, Australia T. Sawbridge La Trobe University, Australia E. K. Ong La Trobe University, Australia C. G. Love Victorian Bioinformatics Consortium, Australia T. A. Erwin La Trobe University, Australia See next page for additional authors Follow this and additional works at: https://uknowledge.uky.edu/igc  Part of the Agricultural Science Commons, Agronomy and Crop Sciences Commons, Plant Biology Commons, Plant Pathology Commons, Soil Science Commons, and the Weed Science Commons This document is available at https://uknowledge.uky.edu/igc/20/satellitesymposium5/69 The XX International Grassland Congress took place in Ireland and the UK in June-July 2005. The main congress took place in Dublin from 26 June to 1 July and was followed by post congress satellite workshops in Aberystwyth, Belfast, Cork, Glasgow and Oxford. The meeting was hosted by the Irish Grassland Association and the British Grassland Society. Proceedings Editor: D. A. McGilloway Publisher: Wageningen Academic Publishers, The Netherlands © Wageningen Academic Publishers, The Netherlands, 2005 The copyright holder has granted the permission for posting the proceedings here. This Event is brought to you for free and open access by the Plant and Soil Sciences at UKnowledge. It has been accepted for inclusion in International Grassland Congress Proceedings by an authorized administrator of UKnowledge. For more information, please contact UKnowledge@lsv.uky.edu. Presenter Information G. C. Spangenberg, T. Sawbridge, E. K. Ong, C. G. Love, T. A. Erwin, E. G. Logan, and D. Edwards This event is available at UKnowledge: https://uknowledge.uky.edu/igc/20/satellitesymposium5/69 Molecular breeding for the genetic improvement of forage crops and turf 201Ryegrass ASTRA: a web-based resource for Lolium EST analysis  G.C. Spangenberg1,2,3, T. Sawbridge1,2, E.K. Ong1, C.G. Love1,2, T.A. Erwin1,2, E.G. Logan1,2 and D. Edwards1,2,3  1Primary Industries Research Victoria, Plant Biotechnology Centre, La Trobe University, Bundoora, Victoria 3086, Australia  2Victorian Bioinformatics Consortium, Australia 3Molecular Plant Breeding Cooperative Research Centre, Australia Email: german.spangenberg@dpi.vic.gov.au  Keywords: perennial ryegrass, expressed sequence tags (ESTs), gene annotation, bioinformatics ASTRA database, simple sequence repeats (SSRs), single nucleotide polymorphisms (SNPs)  Introduction Perennial ryegrass (Lolium perenne L.) is a major grass species of temperate pastoral agriculture.   Materials and methods A resource of 44,524 perennial ryegrass expressed sequence tags (ESTs) from single pass DNA sequencing of randomly selected clones from 29 cDNA libraries representing a range of plant organs and developmental stages was generated (Sawbridge et al., 2003). Each of these sequences has been annotated by comparison to the GenBank and SwissProt public sequence databases. Automated intermediate Gene Ontology (GO) annotation has also been determined.   Results and conclusions Sequence annotation was determined for 80%, 53% and 50% of sequences using GenBank, SwissProt and GO annotation respectively. Only 17% of sequences were determined to have no comparative annotation and thus appear to be unique to ryegrass. EST redundancy was resolved through assembly with CAP3, identifying at total of 12,170 unigenes within this dataset. All sequences and annotation are maintained within an ASTRA format MySQL database, with web based access for text searching, BLAST sequence comparison and Gene Ontology hierarchical tree browsing. Each ryegrass sequence was mapped onto an EnsEMBL genome viewer for comparison with the complete genome sequence of rice and expressed sequences from related species.   In total 3,214 ryegrass simple sequence repeat (SSR) molecular markers have been identified using SSRPrimer and specific PCR amplification primers were designed. A total of 2,716 candidate single nucleotide polymorphism (SNP) molecular markers and 345 insertion deletions (InDels) molecular markers were also identified in 493 loci using AutoSNP. The integration of different analysis tools and the resulting data within a central resource allow users to identify novel candidate genes and associated molecular genetic markers that can be applied to functional genomics and germplasm enhancement in this agronomically important forage and turf grass.                    Figure 1 Annotation of ryegrass genes within the ASTRA database  Reference Sawbridge, T., Ong, E.K., Binnion, C., Emmerling, M., McInnes, R., Meath, K., Nguyen, N., Nunan, K., O’Neill, M., O’Toole, F., Rhodes, C., Simmonds, J., Tian, P., Wearne, K., Webster, T., Winkworth, A. and Spangenberg, G. (2003). Generation and analysis of expressed sequence tags in perennial ryegrass (Lolium perenne L.). Plant Science, 165, 1089-1100. 48% GenBank 80% SwissProt Gene  Ontology 2% 53% 50% 3% 0% No annotation 17% 

Ryegrass ASTRA: a Web-Based Resource for \u3cem\u3eLolium\u3c/em\u3e EST Analysis

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Ryegrass ASTRA: a Web-Based Resource for \u3cem\u3eLolium\u3c/em\u3e EST Analysis

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