Transcript abundance – Association transcriptomics

Transcriptome sequencing also provides us with information about the level of individual gene expression.  Our interest has been to explore the potential links between the level of gene expression and trait phenotype e.g. plant weight, seed yield, especially with respect to the phenomenon of heterosis (“hybrid vigour”).  Our Association transcriptomics programme is conducted in collaboration with Martin Trick, JIC.

Initial work, in collaboration with technology management company PBL, led to the development of a Brassica microarray to measure gene expression, this has now been superseded by the use of Illumina mRNA sequencing data.  PBL also supported the development of proprietary software for this application.

Patent

I. Bancroft, D.R. Stokes, C.L. Morgan, F. Fraser and C.M. O’Neill. 
PCT/GB2007/001194. 
Prediction of heterosis and other traits by transcriptome analysis.

Relevant Publications:

An association transcriptomics approach to the prediction of hybrid performance.
Stokes D, Fraser F, Morgan C, O'Neill CM, Dreos R, Magusin A, Szalma S and Bancroft I.
Molecular Breeding (2010) 26:91-106

A newly-developed community microarray resource for transcriptome profiling in Brassica species enables the confirmation of Brassica-specific expressed sequences.
Trick M, Cheung F, Drou N, Fraser F, Lobenhofer EK, Hurban P, Magusin A, Town CD and Bancroft I.
BMC Plant Biology (2009) 9:50