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Investigating trait ontologies to facilitate integrating phenotype and genome sequence level information in wheat

Appels, R. (2011) Investigating trait ontologies to facilitate integrating phenotype and genome sequence level information in wheat. In: XVIII International Botanical Congress IBC2011, 23 - 30 July, Melbourne, Australia.

Abstract

Commercially important crops such as wheat (Triticum aestivum L.) have an extensive history of data collection, relating phenotype to genetic information. The catalogue of gene symbols for wheat (http://www.shigen.nig.ac.jp/wheat/komugi/genes/symbo lClassList.jsp, edited by R.A. McIntosh), provides a well- (meaning manually) curated assessment of the genetic studies carried out to map traits of interest to genetic maps. These traits are assigned symbols, and an example of an entry is: Pre-harvest sprouting QTL: Several QTL for falling number and alpha-amylase activity, two indicators for pre-harvest sprouting resistance, were identified in {0169}. The most significant were associated with Xglk699-2A and Xsfr4(NBS)-2A, Xglk80-3A and Xpsr1054-3A, Xpsr1194-5A and Xpsr918-5A, Xpsr644-5A and Xpsr945-5A, Xpsr8(Cxp3)-6A and Xpsr563-6A, and Xpsr350-7B and Xbzh232(Tha)-7B {0169}. Typically, a trait such as pre-harvest sprouting will have several synonyms, such as sprouting index (QSi.crc-5D), dormancy (Q.SD1), or pre-harvest sprouting (Qphs.ocs- 3A.2), which need to be captured for an effective analysis of published information. In order to crossreference genome sequence information to trait/phenotype studies, the available information in wheat is now cross-referenced to detailed consensus molecular genetic maps (http://ccg.murdoch.edu.au/cmap/ccg-live/cgibin/ cmap/viewer) in the CMap software utilized by GRAMENE (http://www.gramene.org/). In this presentation, the experience of developing trait ontologies for wheat, using the information established for rice, will be discussed in the context of relating the CMap-based information that locates published QTL for traits to the genome sequence of wheat. The sequence of a complex genome such as wheat has been challenging to develop, but several new technologies are now converging to establish draft sequence-level definitions of the gene-space.

Publication Type: Conference Item
Murdoch Affiliation: Centre for Comparative Genomics
URI: http://researchrepository.murdoch.edu.au/id/eprint/20030
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