Projects per year
Abstract
Background
White clover is a short-lived perennial whose persistence is greatly affected by abiotic stresses, particularly drought. An understanding of its molecular response to water deficit and recovery following re-hydration is of paramount importance to identify targets for the breeding of tolerant varieties.
Results
We created a white clover reference transcriptome of 16,193 contigs by de novo and reference-based assembly of Illumina reads from four SSH libraries (forward and reverse libraries for each treatment) constructed from leaf material of white clover at the onset of drought and recovery. Reads from individual libraries were then mapped to the reference transcriptome and processed comparing expression level data to generate four robust sets of transcripts induced and repressed in the leaves subjected to and recovering from water stress. The differentially expressed transcripts were functionally annotated and mapped to biological processes and pathways.
Conclusions
The work presented in this paper provides a simple pipeline for the processing of data generated by deep sequencing of SSH libraries and the first large scale molecular analysis of the white clover response to drought stress and recovery.
White clover is a short-lived perennial whose persistence is greatly affected by abiotic stresses, particularly drought. An understanding of its molecular response to water deficit and recovery following re-hydration is of paramount importance to identify targets for the breeding of tolerant varieties.
Results
We created a white clover reference transcriptome of 16,193 contigs by de novo and reference-based assembly of Illumina reads from four SSH libraries (forward and reverse libraries for each treatment) constructed from leaf material of white clover at the onset of drought and recovery. Reads from individual libraries were then mapped to the reference transcriptome and processed comparing expression level data to generate four robust sets of transcripts induced and repressed in the leaves subjected to and recovering from water stress. The differentially expressed transcripts were functionally annotated and mapped to biological processes and pathways.
Conclusions
The work presented in this paper provides a simple pipeline for the processing of data generated by deep sequencing of SSH libraries and the first large scale molecular analysis of the white clover response to drought stress and recovery.
Original language | English |
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Article number | 213 |
Journal | Frontiers in Plant Science |
Volume | 8 |
DOIs | |
Publication status | Published - 23 Feb 2017 |
Keywords
- white clover
- drought
- recovery
- SSH libraries
- MiSeq
Fingerprint
Dive into the research topics of 'Deep sequencing of Suppression Subtractive Hybridisation drought and recovery libraries of the non-model crop Trifolium repens L.'. Together they form a unique fingerprint.Projects
- 3 Finished
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Bioinformatics and genomic and phenomic platform development
Armstead, I. (PI), Boyle, R. (PI), Doonan, J. (PI), Fernandez Fuentes, N. (PI), Gay, A. (PI), Hegarty, M. (PI), Huang, L. (PI), Neal, M. (PI), Swain, M. (PI) & Thomas, I. (PI)
01 Apr 2012 → 31 Mar 2017
Project: Externally funded research
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C3G: Lolium and Trifolium genetics, genomics and germplasm development
Armstead, I. (PI), Jenkins, G. (PI), Marshall, A. (PI), Skot, L. (PI), Thomas, I. (PI) & Thorogood, D. (PI)
01 Apr 2012 → 31 Mar 2017
Project: Externally funded research
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Introgression and wide hybrid genetics, genomics and germplasm development in Lolium/Festuca (Festulolium) and white clover
Armstead, I. (PI)
01 Apr 2012 → 31 Mar 2017
Project: Externally funded research