Identification of Genes Differentially Expressed in Response to Cold in <i>Pisum sativum</i> Using RNA Sequencing Analyses
Low temperature stress affects growth and development in pea (<i>Pisum sativum</i> L.) and decreases yield. In this study, RNA sequencing time series analyses performed on lines, Champagne frost-tolerant and Térèse frost-sensitive, during a low temperature treatment ver...
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| Format: | Article |
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MDPI AG
2019-08-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/8/8/288 |
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| author | Nasser Bahrman Emilie Hascoët Odile Jaminon Frédéric Dépta Jean-François Hû Olivier Bouchez Isabelle Lejeune-Hénaut Bruno Delbreil Sylvain Legrand |
| author_facet | Nasser Bahrman Emilie Hascoët Odile Jaminon Frédéric Dépta Jean-François Hû Olivier Bouchez Isabelle Lejeune-Hénaut Bruno Delbreil Sylvain Legrand |
| author_sort | Nasser Bahrman |
| collection | DOAJ |
| description | Low temperature stress affects growth and development in pea (<i>Pisum sativum</i> L.) and decreases yield. In this study, RNA sequencing time series analyses performed on lines, Champagne frost-tolerant and Térèse frost-sensitive, during a low temperature treatment versus a control condition, led us to identify 4981 differentially expressed genes. Thanks to our experimental design and statistical analyses, we were able to classify these genes into three sets. The first one was composed of 2487 genes that could be related to the constitutive differences between the two lines and were not regulated during cold treatment. The second gathered 1403 genes that could be related to the chilling response. The third set contained 1091 genes, including genes that could be related to freezing tolerance. The identification of differentially expressed genes related to cold, oxidative stress, and dehydration responses, including some transcription factors and kinases, confirmed the soundness of our analyses. In addition, we identified about one hundred genes, whose expression has not yet been linked to cold stress. Overall, our findings showed that both lines have different characteristics for their cold response (chilling response and/or freezing tolerance), as more than 90% of differentially expressed genes were specific to each of them. |
| first_indexed | 2024-04-11T16:25:57Z |
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| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-04-11T16:25:57Z |
| publishDate | 2019-08-01 |
| publisher | MDPI AG |
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| series | Plants |
| spelling | doaj.art-9316709f7fb84a659f3187e2c31943b62022-12-22T04:14:12ZengMDPI AGPlants2223-77472019-08-018828810.3390/plants8080288plants8080288Identification of Genes Differentially Expressed in Response to Cold in <i>Pisum sativum</i> Using RNA Sequencing AnalysesNasser Bahrman0Emilie Hascoët1Odile Jaminon2Frédéric Dépta3Jean-François Hû4Olivier Bouchez5Isabelle Lejeune-Hénaut6Bruno Delbreil7Sylvain Legrand8ICV—Institut Charles Viollette, EA 7394, USC 1411, Univ. Lille, F-59000 Lille, FranceICV—Adaptation au Froid du Pois, USC 1411, INRA, F-80300 Péronne, FranceICV—Adaptation au Froid du Pois, USC 1411, INRA, F-80300 Péronne, FranceGCIE, UE 0972, INRA, F-80203 Péronne, FranceGCIE, UE 0972, INRA, F-80203 Péronne, FranceGeT-PlaGe, Genotoul, US 1426, INRA, F-31326 Castanet-Tolosan, FranceICV—Adaptation au Froid du Pois, USC 1411, INRA, F-80300 Péronne, FranceICV—Institut Charles Viollette, EA 7394, USC 1411, Univ. Lille, F-59000 Lille, FranceEvo-Eco-Paleo, UMR 8198, Univ. Lille, CNRS, F-59000 Lille, FranceLow temperature stress affects growth and development in pea (<i>Pisum sativum</i> L.) and decreases yield. In this study, RNA sequencing time series analyses performed on lines, Champagne frost-tolerant and Térèse frost-sensitive, during a low temperature treatment versus a control condition, led us to identify 4981 differentially expressed genes. Thanks to our experimental design and statistical analyses, we were able to classify these genes into three sets. The first one was composed of 2487 genes that could be related to the constitutive differences between the two lines and were not regulated during cold treatment. The second gathered 1403 genes that could be related to the chilling response. The third set contained 1091 genes, including genes that could be related to freezing tolerance. The identification of differentially expressed genes related to cold, oxidative stress, and dehydration responses, including some transcription factors and kinases, confirmed the soundness of our analyses. In addition, we identified about one hundred genes, whose expression has not yet been linked to cold stress. Overall, our findings showed that both lines have different characteristics for their cold response (chilling response and/or freezing tolerance), as more than 90% of differentially expressed genes were specific to each of them.https://www.mdpi.com/2223-7747/8/8/288peacold stresschillingacclimationfreezing tolerancetranscriptomeRNA-seq |
| spellingShingle | Nasser Bahrman Emilie Hascoët Odile Jaminon Frédéric Dépta Jean-François Hû Olivier Bouchez Isabelle Lejeune-Hénaut Bruno Delbreil Sylvain Legrand Identification of Genes Differentially Expressed in Response to Cold in <i>Pisum sativum</i> Using RNA Sequencing Analyses Plants pea cold stress chilling acclimation freezing tolerance transcriptome RNA-seq |
| title | Identification of Genes Differentially Expressed in Response to Cold in <i>Pisum sativum</i> Using RNA Sequencing Analyses |
| title_full | Identification of Genes Differentially Expressed in Response to Cold in <i>Pisum sativum</i> Using RNA Sequencing Analyses |
| title_fullStr | Identification of Genes Differentially Expressed in Response to Cold in <i>Pisum sativum</i> Using RNA Sequencing Analyses |
| title_full_unstemmed | Identification of Genes Differentially Expressed in Response to Cold in <i>Pisum sativum</i> Using RNA Sequencing Analyses |
| title_short | Identification of Genes Differentially Expressed in Response to Cold in <i>Pisum sativum</i> Using RNA Sequencing Analyses |
| title_sort | identification of genes differentially expressed in response to cold in i pisum sativum i using rna sequencing analyses |
| topic | pea cold stress chilling acclimation freezing tolerance transcriptome RNA-seq |
| url | https://www.mdpi.com/2223-7747/8/8/288 |
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