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Deep Super-SAGE transcriptomic analysis of cold acclimation in lentil (Lens culinaris Medik.)

BACKGROUND: Frost is one of the main abiotic stresses limiting plant distribution and crop production. To cope with the stress, plants evolved adaptations known as cold acclimation or chilling tolerance to maximize frost tolerance. Cold acclimation is a progressive acquisition of freezing tolerance...

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Autores principales: Barrios, Abel, Caminero, Constantino, García, Pedro, Krezdorn, Nicolas, Hoffmeier, Klaus, Winter, Peter, Pérez de la Vega, Marcelino
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5493078/
https://www.ncbi.nlm.nih.gov/pubmed/28666411
http://dx.doi.org/10.1186/s12870-017-1057-8
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author Barrios, Abel
Caminero, Constantino
García, Pedro
Krezdorn, Nicolas
Hoffmeier, Klaus
Winter, Peter
Pérez de la Vega, Marcelino
author_facet Barrios, Abel
Caminero, Constantino
García, Pedro
Krezdorn, Nicolas
Hoffmeier, Klaus
Winter, Peter
Pérez de la Vega, Marcelino
author_sort Barrios, Abel
collection PubMed
description BACKGROUND: Frost is one of the main abiotic stresses limiting plant distribution and crop production. To cope with the stress, plants evolved adaptations known as cold acclimation or chilling tolerance to maximize frost tolerance. Cold acclimation is a progressive acquisition of freezing tolerance by plants subjected to low non-freezing temperatures which subsequently allows them to survive exposure to frost. Lentil is a cool season grain legume that is challenged by winter frost in some areas of its cultivation. RESULTS: To better understand the genetic base of frost tolerance differential gene expression in response to cold acclimation was investigated. Recombinant inbred lines (RILs) from the cross Precoz x WA8649041 were first classified as cold tolerant or cold susceptible according to their response to temperatures between −3 to −15 °C. Then, RILs from both extremes of the response curve were cold acclimated and the leaf transcriptomes of two bulks each of eight frost tolerant and seven cold susceptible RILs were investigated by Deep Super-SAGE transcriptome profiling. Thus, four RNA bulks were analysed: the acclimated susceptible, the acclimated tolerant and the respective controls (non-acclimated susceptible and non-acclimated tolerant). Approximately 16.5 million 26 nucleotide long Super-SAGE tags were sequenced in the four sets (between ~3 and 5.4 millions). In total, 133,077 different unitags, each representing a particular transcript isoform, were identified in these four sets. Tags which showed a significantly different abundance in any of the bulks (fold change ≥4.0 and a significant p-value <0.001) were selected and used to identify the corresponding lentil gene sequence. Three hundred of such lentil sequences were identified. Most of their known homologs coded for glycine-rich, cold and drought-regulated proteins, dormancy-associated proteins, proline-rich proteins (PRPs) and other membrane proteins. These were generally but not exclusively over-expressed in the acclimated tolerant lines. CONCLUSIONS: This set of candidate genes implicated in the response to frost in lentil represents an useful base for deeper and more detailed investigations into this important agronomic trait in future. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12870-017-1057-8) contains supplementary material, which is available to authorized users.
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spelling pubmed-54930782017-06-30 Deep Super-SAGE transcriptomic analysis of cold acclimation in lentil (Lens culinaris Medik.) Barrios, Abel Caminero, Constantino García, Pedro Krezdorn, Nicolas Hoffmeier, Klaus Winter, Peter Pérez de la Vega, Marcelino BMC Plant Biol Research Article BACKGROUND: Frost is one of the main abiotic stresses limiting plant distribution and crop production. To cope with the stress, plants evolved adaptations known as cold acclimation or chilling tolerance to maximize frost tolerance. Cold acclimation is a progressive acquisition of freezing tolerance by plants subjected to low non-freezing temperatures which subsequently allows them to survive exposure to frost. Lentil is a cool season grain legume that is challenged by winter frost in some areas of its cultivation. RESULTS: To better understand the genetic base of frost tolerance differential gene expression in response to cold acclimation was investigated. Recombinant inbred lines (RILs) from the cross Precoz x WA8649041 were first classified as cold tolerant or cold susceptible according to their response to temperatures between −3 to −15 °C. Then, RILs from both extremes of the response curve were cold acclimated and the leaf transcriptomes of two bulks each of eight frost tolerant and seven cold susceptible RILs were investigated by Deep Super-SAGE transcriptome profiling. Thus, four RNA bulks were analysed: the acclimated susceptible, the acclimated tolerant and the respective controls (non-acclimated susceptible and non-acclimated tolerant). Approximately 16.5 million 26 nucleotide long Super-SAGE tags were sequenced in the four sets (between ~3 and 5.4 millions). In total, 133,077 different unitags, each representing a particular transcript isoform, were identified in these four sets. Tags which showed a significantly different abundance in any of the bulks (fold change ≥4.0 and a significant p-value <0.001) were selected and used to identify the corresponding lentil gene sequence. Three hundred of such lentil sequences were identified. Most of their known homologs coded for glycine-rich, cold and drought-regulated proteins, dormancy-associated proteins, proline-rich proteins (PRPs) and other membrane proteins. These were generally but not exclusively over-expressed in the acclimated tolerant lines. CONCLUSIONS: This set of candidate genes implicated in the response to frost in lentil represents an useful base for deeper and more detailed investigations into this important agronomic trait in future. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12870-017-1057-8) contains supplementary material, which is available to authorized users. BioMed Central 2017-06-30 /pmc/articles/PMC5493078/ /pubmed/28666411 http://dx.doi.org/10.1186/s12870-017-1057-8 Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Barrios, Abel
Caminero, Constantino
García, Pedro
Krezdorn, Nicolas
Hoffmeier, Klaus
Winter, Peter
Pérez de la Vega, Marcelino
Deep Super-SAGE transcriptomic analysis of cold acclimation in lentil (Lens culinaris Medik.)
title Deep Super-SAGE transcriptomic analysis of cold acclimation in lentil (Lens culinaris Medik.)
title_full Deep Super-SAGE transcriptomic analysis of cold acclimation in lentil (Lens culinaris Medik.)
title_fullStr Deep Super-SAGE transcriptomic analysis of cold acclimation in lentil (Lens culinaris Medik.)
title_full_unstemmed Deep Super-SAGE transcriptomic analysis of cold acclimation in lentil (Lens culinaris Medik.)
title_short Deep Super-SAGE transcriptomic analysis of cold acclimation in lentil (Lens culinaris Medik.)
title_sort deep super-sage transcriptomic analysis of cold acclimation in lentil (lens culinaris medik.)
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5493078/
https://www.ncbi.nlm.nih.gov/pubmed/28666411
http://dx.doi.org/10.1186/s12870-017-1057-8
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