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

Abstract

BackgroundFrost 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.ResultsTo 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.ConclusionsThis 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 materialThe online version of this article (doi:10.1186/s12870-017-1057-8) contains supplementary material, which is available to authorized users.

Genome wide transcriptome analysis reveals vital role of heat responsive genes in regulatory mechanisms of lentil (Lens culinaris Medikus)

“…Understanding of underlying molecular mechanism of heat tolerance is still unknown in lentil. However, some reports shedding light on molecular mechanisms of other abiotic stresses like drought and cold are available 7,70 . Transcriptome analysis may provide an overview of novel genes and regulatory networks linked with heat tolerance mechanism in lentil.…”

In-Cold Exposure to Z-3-Hexenal Provides Protection Against Ongoing Cold Stress in Zea mays

“…LEAs, like PROTs, appear to bind preferentially to cytoplasmic facing membrane lipids, and stabilize these structures to prevent protein aggregation [20,24,36,37,38]. Little is known about the role of the adhesive/proline-rich proteins (APRPs) and low temperature inducible proteins (LTIs) in the cold stress response, however, both were found to accumulate in plants under cold stress, strongly suggesting that they have a protective function under these conditions [39,40,41,42,43].…”

Green leaf volatiles protect maize (Zea mays) seedlings against damage from cold stress

“…LEAs preferentially bind to cytoplasmic facing membrane lipids to stabilize these structures and prevent protein aggregation (Bray, ; Cuming, ; Roberts, DeSimone, Lingle, & Dure III, ; Tolleter et al, ; Welin et al, ). Less is known about what role the adhesive/proline‐rich proteins ( APRPs ) and low temperature inducible proteins ( LTIs ) might play in the plant cold stress response; however, both are known to accumulate in plants under cold stress and several studies have suggested a protective function for APRPs and LTIs under these conditions (Barrios et al, ; Kawarazaki et al, ; Kim et al, ; Li et al, ; Recchia, Caldas, Beraldo, da Silva, & Tsai, ; Tseng, Hong, Yu, & Ho, ).…”

“…LEAs preferentially bind to cytoplasmic facing membrane lipids to stabilize these structures and prevent protein aggregation (Bray, 1993;Cuming, 1999;Roberts, DeSimone, Lingle, & Dure III, 1993;Tolleter et al, 2010;Welin et al, 1994). have suggested a protective function for APRPs and LTIs under these conditions (Barrios et al, 2017;Kawarazaki et al, 2013;Kim et al, 2004;Li et al, 2016;Recchia, Caldas, Beraldo, da Silva, & Tsai, 2013;Tseng, Hong, Yu, & Ho, 2013).…”