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

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

Open Access Journal; Published online: 23 Feb. 2017

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Main Authors: Bisaga, M., Lowe, M., Hegarty, M., Abberton, Michael T., Ravagnani, A.
Format: Journal Article biblioteca
Language:English
Published: Frontiers Media 2017
Subjects:white clover, drought, recovery, ssh libraries, miseq, genometic, rna extraction, cdna synthesis, sqrt-pcr, hybridization,
Online Access:https://hdl.handle.net/10568/83494
https://doi.org/10.3389/fpls.2017.00213
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spelling dig-cgspace-10568-834942023-12-08T19:36:04Z Deep sequencing of Suppression Subtractive Hybridisation drought and recovery libraries of the non-model crop Trifolium repens L. Bisaga, M. Lowe, M. Hegarty, M. Abberton, Michael T. Ravagnani, A. white clover drought recovery ssh libraries miseq genometic rna extraction cdna synthesis sqrt-pcr hybridization Open Access Journal; Published online: 23 Feb. 2017 White 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. 2017 2017-09-13T14:23:31Z 2017-09-13T14:23:31Z Journal Article Bisaga, 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. 1664-462X https://hdl.handle.net/10568/83494 https://doi.org/10.3389/fpls.2017.00213 BIOTECH & PLANT BREEDING en Open Access 1-39 application/pdf Frontiers Media Frontiers in Plant Science
institution CGIAR
collection DSpace
country Francia
countrycode FR
component Bibliográfico
access En linea
databasecode dig-cgspace
tag biblioteca
region Europa del Oeste
libraryname Biblioteca del CGIAR
language English
topic white clover
drought
recovery
ssh libraries
miseq
genometic
rna extraction
cdna synthesis
sqrt-pcr
hybridization
white clover
drought
recovery
ssh libraries
miseq
genometic
rna extraction
cdna synthesis
sqrt-pcr
hybridization
spellingShingle white clover
drought
recovery
ssh libraries
miseq
genometic
rna extraction
cdna synthesis
sqrt-pcr
hybridization
white clover
drought
recovery
ssh libraries
miseq
genometic
rna extraction
cdna synthesis
sqrt-pcr
hybridization
Bisaga, M.
Lowe, M.
Hegarty, M.
Abberton, Michael T.
Ravagnani, A.
Deep sequencing of Suppression Subtractive Hybridisation drought and recovery libraries of the non-model crop Trifolium repens L.
description Open Access Journal; Published online: 23 Feb. 2017
format Journal Article
topic_facet white clover
drought
recovery
ssh libraries
miseq
genometic
rna extraction
cdna synthesis
sqrt-pcr
hybridization
author Bisaga, M.
Lowe, M.
Hegarty, M.
Abberton, Michael T.
Ravagnani, A.
author_facet Bisaga, M.
Lowe, M.
Hegarty, M.
Abberton, Michael T.
Ravagnani, A.
author_sort Bisaga, M.
title Deep sequencing of Suppression Subtractive Hybridisation drought and recovery libraries of the non-model crop Trifolium repens L.
title_short Deep sequencing of Suppression Subtractive Hybridisation drought and recovery libraries of the non-model crop Trifolium repens L.
title_full Deep sequencing of Suppression Subtractive Hybridisation drought and recovery libraries of the non-model crop Trifolium repens L.
title_fullStr Deep sequencing of Suppression Subtractive Hybridisation drought and recovery libraries of the non-model crop Trifolium repens L.
title_full_unstemmed Deep sequencing of Suppression Subtractive Hybridisation drought and recovery libraries of the non-model crop Trifolium repens L.
title_sort deep sequencing of suppression subtractive hybridisation drought and recovery libraries of the non-model crop trifolium repens l.
publisher Frontiers Media
publishDate 2017
url https://hdl.handle.net/10568/83494
https://doi.org/10.3389/fpls.2017.00213
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AT hegartym deepsequencingofsuppressionsubtractivehybridisationdroughtandrecoverylibrariesofthenonmodelcroptrifoliumrepensl
AT abbertonmichaelt deepsequencingofsuppressionsubtractivehybridisationdroughtandrecoverylibrariesofthenonmodelcroptrifoliumrepensl
AT ravagnania deepsequencingofsuppressionsubtractivehybridisationdroughtandrecoverylibrariesofthenonmodelcroptrifoliumrepensl
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