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Deep sequencing of Suppression Subtractive Hybridisation drought and recovery libraries of the non-model crop Trifolium repens L.

dc.contributor.authorBisaga, M.
dc.contributor.authorLowe, M.
dc.contributor.authorHegarty, M.
dc.contributor.authorAbberton, M.T.
dc.contributor.authorRavagnani, A.
dc.date.accessioned2019-12-04T11:10:15Z
dc.date.available2019-12-04T11:10:15Z
dc.date.issued2017
dc.identifier.citationBisaga, M., Lowe, M., Hegarty, M., Abberton, M. & Ravagnani, A. (2017). Deep sequencing of Suppression Subtractive Hybridisation drought and recovery libraries of the non-model crop Trifolium repens L. Frontiers in Plant Science, 8(213), 1-38.
dc.identifier.issn1664-462X
dc.identifier.urihttps://hdl.handle.net/20.500.12478/2047
dc.descriptionOpen Access Journal; Published online: 23 Feb. 2017
dc.description.abstractWhite clover is a short-lived perennial whose persistence is greatly affected by abiotic stresses, particularly drought. The aim of this work was to characterize its molecular response to water deficit and recovery following re-hydration to identify targets for the breeding of tolerant varieties. We created a white clover reference transcriptome of 16,193 contigs by deep sequencing (mean base coverage 387x) four Suppression Subtractive Hybridization (SSH) libraries (a forward and a reverse library for each treatment) constructed from young leaf tissue of white clover at the onset of the response to drought and recovery. Reads from individual libraries were then mapped to the reference transcriptome and processed comparing expression level data. The pipeline generated four robust sets of transcripts induced and repressed in the leaves of plants subjected to water deficit stress (6,937 and 3,142, respectively) and following re-hydration (6,695 and 4,897, respectively). Semi-quantitative polymerase chain reaction was used to verify the expression pattern of 16 genes. The differentially expressed transcripts were functionally annotated and mapped to biological processes and pathways. In agreement with similar studies in other crops, the majority of transcripts up-regulated in response to drought belonged to metabolic processes, such as amino acid, carbohydrate, and lipid metabolism, while transcripts involved in photosynthesis, such as components of the photosystem and the biosynthesis of photosynthetic pigments, were up-regulated during recovery. The data also highlighted the role of raffinose family oligosaccharides (RFOs) and the possible delayed response of the flavonoid pathways in the initial response of white clover to water withdrawal. The work presented in this paper is to our knowledge the first large scale molecular analysis of the white clover response to drought stress and re-hydration. The data generated provide a valuable genomic resource for marker discovery and ultimately for the improvement of white clover.
dc.description.sponsorshipBiotechnology and Biological Sciences Research Council, United Kingdom
dc.format.extent1-39
dc.language.isoen
dc.subjectWhite Clover
dc.subjectDrought
dc.subjectRecovery
dc.subjectSsh Libraries
dc.subjectMiseq
dc.subjectGenometic
dc.subjectRna Extraction
dc.subjectCdna Synthesis
dc.subjectSqrt-Pcr
dc.subjectHybridization
dc.titleDeep sequencing of Suppression Subtractive Hybridisation drought and recovery libraries of the non-model crop Trifolium repens L.
dc.typeJournal Article
dc.description.versionPeer Review
cg.contributor.crpRoots, Tubers and Bananas
cg.contributor.affiliationAberystwyth University
cg.contributor.affiliationInternational Institute of Tropical Agriculture
cg.researchthemeBIOTECH & PLANT BREEDING
cg.isijournalISI Journal
cg.authorship.typesCGIAR and advanced research institute
cg.iitasubjectPlant Breeding
cg.iitasubjectPlant Genetic Resources
cg.journalFrontiers in Plant Science
cg.howpublishedFormally Published
cg.accessibilitystatusOpen Access
local.dspaceid86043
cg.targetaudienceScientists
cg.identifier.doihttps://dx.doi.org/10.3389/fpls.2017.00213


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