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The up-regulation of elongation factors in the barley leaf and the down-regulation of nucleosome assembly genes in the crown are both associated with the expression of frost tolerance

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Abstract

We report a series of microarray-based leaf and crown transcriptome comparisons involving three barley cultivars (cvs. Luxor, Igri and Atlas 68) which express differing degrees of frost tolerance. The transcripts were obtained following the exposure of seedlings to low (above and below zero) temperatures, aiming to identify those genes and signalling/metabolic pathways which are associated with frost tolerance. Both the leaves and the crowns responded to low temperature by the up-regulation of a suite of abscisic acid (ABA)-responsive genes, most of which have already been recognized as components of the plant low temperature response. The inter-cultivar comparison indicated that genes involved in maintaining the leaf's capacity to synthesize protein and to retain chloroplast activity were important for the expression of frost tolerance. In the crown, the repression of genes associated with nucleosome assembly and transposon regulation were the most relevant transcriptional changes associated with frost tolerance, highlighting the role of gene repression in the cold acclimation response.

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Acknowledgments

This research was funded by the Czech Republic National Agency for Agricultural Research (project no. QH 81287), by the Czech Ministry of Agriculture (project no. Mze0002700604), by the Ministry of Education, Youth and Sports (project no. OC09032) and by the Italian Ministry of Agriculture, Special Project ESPLORA.

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Authors and Affiliations

  1. Department of Molecular Biology, Crop Research Institute, v.v.i., Drnovská 507, 161 06, Prague 6, Czech Republic

    Anna Janská, Jiří Zámečník & Jaroslava Ovesná

  2. Faculty of Science, Charles University in Prague, Viničná 5, 128 44, Prague 2, Czech Republic

    Anna Janská

  3. Department of Biological and Environmental Sciences and Technologies, University of Salento, Ecoteckne prov.le Monteroni-Lecce, 73100, Lecce, Italy

    Alessio Aprile & Luigi de Bellis

  4. Consiglio per la Ricerca e la sperimentazione in Agricoltura, Genomics Research Centre, via S. Protaso, 302, I-29017, Fiorenzuola d’Arda, PC, Italy

    Luigi Cattivelli

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  1. Anna Janská
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  4. Jiří Zámečník
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Correspondence to Anna Janská.

Electronic supplementary material

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Supplementary Fig. 1

Hybridization quality. The plots show the mean intensity of each probe across a specific probe set, ordered from the 5′ to the 3′ end. All curves have a similar slope, implying that the hybridization quality was uniformly high. (GIF 408 kb)

High resolution image (TIFF 3,863 kb)

Supplementary Table 1

A complete list of genes differentially transcribed in (a) the leaf and (b) the crown. The genes have been classified into Lists/Groups and Clusters according to Fig. 3 (leaf) and Fig. 6 (crown). (1A 26,243 kb)

(1B 25,613 kb)

Supplementary Table 2

Genes transcribed in (a) the leaf and (b) the crown which map to regions harboring known QTL for frost tolerance (Fisk et al. 2013). Six regions were targeted: (1, 2) chromosome 1H 0–7 cM and 35–55 cM (the latter interval is the site of Fr-H3); (3) chromosome 4H 120–140 cM; (4, 5) chromosome 5H 85–110 cM (site of Fr-H2) and 129–154 cM (site of both Vrn-H1 and Fr-H1); and (6) chromosome 7H 132–142 cM. Transcription signal derived from microarray analysis. The classification of the genes according to list/group and cluster is given in Figs. 3 (leaf) and 6 (crown). (XLS 27,870 kb)

(XLS 27,239 kb)

Supplementary Table 3

Genes differentially transcribed (DTGs) in (a) the leaf and (b) the crown which map to regions harboring known QTL for frost tolerance (Fisk et al. 2013). Six regions were targeted: (1, 2) chromosome 1H 0–7 cM and 35–55 cM (the latter interval is the site of Fr-H3); (3) chromosome 4H 120–140 cM; (4, 5) chromosome 5H 85–110 cM (site of Fr-H2) and 129–154 cM (site of both Vrn-H1 and Fr-H1); and (6) chromosome 7H 132–142 cM. Transcript abundance derived from microarray analysis. The classification of the genes according to list/group and cluster is given in Figs. 3 (leaf) and 6 (crown). (DOC 219 kb)

(DOC 85 kb)

Supplementary Table 4

Genes differentially transcribed (DTGs) in (a) the leaf and (b) the crown which belong to a particular list/group and cluster, and which map to regions harboring known QTL for frost tolerance (Fisk et al. 2013). The DTGs referred to in the text are marked in bold. Six regions were targeted: (1, 2) chromosome 1H 0–7 cM and 35–55 cM (the latter interval is the site of Fr-H3); (3) chromosome 4H 120–140 cM; (4, 5) chromosome 5H 85–110 cM (site of Fr-H2) and 129–154 cM (site of both Vrn-H1 and Fr-H1); and (6) chromosome 7H 132–142 cM. Transcript abundance derived from microarray analysis. The classification of the genes according to list/group and cluster is given in Figs. 3 (leaf) and 6 (crown). (DOC 118 kb)

(DOC 45 kb)

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Janská, A., Aprile, A., Cattivelli, L. et al. The up-regulation of elongation factors in the barley leaf and the down-regulation of nucleosome assembly genes in the crown are both associated with the expression of frost tolerance. Funct Integr Genomics 14, 493–506 (2014). https://doi.org/10.1007/s10142-014-0377-0

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  • DOI: https://doi.org/10.1007/s10142-014-0377-0

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