Eur.J.Hortic.Sci. 80 (1) 39-46 | DOI: 10.17660/eJHS.2015/80.1.6|
ISSN 1611-4426 print and 1611-4434 online | © ISHS 2015 | European Journal of Horticultural Science | Original article
The effects of drought stress on leaf gene expression during flowering in blackcurrant (Ribes nigrum L.)
N. Čereković1, D. Jarret2, M. Pagter4,1, D.W. Cullen3, J.M. Morris3, P.E. Hedley3, R. Brennan3 and
1 Department of Food Science, Aarhus University, Denmark
2 Mylnefield Research Services Ltd., Invergowrie, Dundee, Scotland, UK
3 The James Hutton Institute, Invergowrie, Dundee, Scotland, UK
4 Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
This study provides genome expression analyses
from the blackcurrant cultivar ‘Ben Gairn’ after five
days of drought stress. RNA Sequencing (RNA-Seq)
data was utilized to generate a non-redundant set of
40,225 predicted transcripts used to design a custom
Ribes microarray. A set of 2,115 differentially
expressed genes were identified during drought
treatment; 429 of these genes were up-regulated,
with 263 showing homology to unique Arabidopsis
thaliana (At) accessions, and 1,686 genes were
down-regulated, with 675 unique At numbers. The
Arabidopsis homologs were analysed for enrichment
of GO (gene ontology) terms using the Term Enrichment
Tool. This showed a number of GO terms highly
enriched in the drought up-regulated and down-regulated
gene lists in GO categories associated with
molecular function, biological process and cellular
component. The identification of several hormone
metabolism, cell wall, cell cycle, and transcription
factor genes indicated that they could play an important
role in the drought stress tolerance response.
The results provide relevant information for focusing
future studies with the aim to develop drought
tolerant cultivars for sustainable production.
cell wall and cell cycle, GO term enrichment analyses,
hormone metabolism genes, Ribes microarray, transcription
Significance of this study
What is already known on this subject?
What are the new findings?
Drought is a major limitation for crop productivity
worldwide and in future periods of water stress are
more likely to occur. Molecular responses to drought
stress are very complex, but our understanding has
rapidly progressed with the identification of thousands
of genes involved in acclimatization and adaptation.
What is the expected impact on horticulture?
Genome expression analyses from blackcurrant
‘Ben Gairn’ after five days of drought stress. Volcano
filtering identified 2,115 differentially expressed
microarray probes; 429 were up-regulated, with 263
showing homology to unique Arabidopsis thaliana
(At) accessions, and 1,686 were down-regulated,
with 675 unique At numbers.
Putative candidate genes involved in drought stress
tolerance of blackcurrant were identified, but require
further, more detailed, studies to confirm their role.
The results provide relevant information for focusing
future studies with the aim to develop drought tolerant
cultivars for sustainable production.
- Abe, H., Urao, T., Ito, T., Seki, M., Shinozaki, K., and Yamaguchi-Shinozaki, K. (2003). Arabidopsis AtMYC2 (bHLH) and AtMYB2 (MYB) Function as Transcriptional Activators in Abscisic Acid Signaling. Plant Cell 15, 63–78.
- Anon. (2013). Meteorological Office Regional Values 2012. Available at: http://www.metoffice.gov.uk/climate/uk/2012/spring/averages.html.
- Blum, A. (2011). Plant Breeding for Water-Limited Environments (New York: Springer), pp. 258.
- Bray, E.A. (2004). Genes commonly regulated by water-deficit stress in Arabidopsis thaliana. J. Exp. Bot. 55, 2331–2341.
- Brennan, R.M. (2008). Currants and gooseberries (Ribes spp.). In Breeding of Temperate Fruit Crops, J. Hancock, ed. (New York: Springer), pp. 177–196.
- Brennan, R., and Graham, J. (2009). Improving fruit quality in Rubus and Ribes through breeding. Funct. Plant Sci. Biotechnol. 3, 22-29.
- Čereković, N., Pagter, M., Kristensen, H.L., Pedersen, H.L., Brennan, R., and Petersen, K.K. (2013). Effects of drought stress during flowering of two pot-grown blackcurrant (Ribes nigrum L.) cultivars. Sci. Hortic. 162, 365–373.
- Čereković, N., Pagter, M., Kristensen, H.L., Brennan, R., and Petersen, K.K. (2014). Effects of deficit irrigation during flower initiation of two blackcurrant (Ribes nigrum L.) cultivars. Sci. Hortic. 168, 193–201.
- Chaves, M.M., Maroco, J.P., and Pereira, J.S. (2003). Understanding plant responses to drought - from genes to the whole plant. Funct. Plant Biol. 30, 239–264.
- Chen, J., Song, Y., Zhang, H., and Zhang, D. (2013). Genome-Wide Analysis of Gene Expression in Response to Drought Stress in Populus simonii. Plant Mol. Biol. Report. 31, 946–962.
- Chinnusamy, V., Zhu, J., and Zhu, J.K. (2007). Cold stress regulation of gene expression in plants. Trends Plant Sci. 12, 444–451.
- Cohen, D., Bogeat-Triboulot, M.B., Tissernt, E., Balzergue, S., Martin-Magniette, M.L., Lelandais, G., Ningre, N., Renou, J.P., Tamby, J.P., Le Thiec, D., and Hummel, I. (2010). Comparative transcriptomics of drought responses in Populus: a meta-analysis of genome-wide expression profiling in mature leaves and root apices across two genotypes. BMC Genomics 11(1), 630. Available at: http://www.biomedcentral.com/1471-2164/11/630.
- Deokar, A.A., Kondawar, V., Jain, P.K., Karuppayil, S.M., Raju, N.L., Vadez, V., Varsheney, R.K., and Srinivasan, R. (2011). Comparative analysis of expressed sequence tags (ESTs) between droughttolerant and -susceptible genotypes of chickpea under terminal drought stress. BMC Plant Biol. 11, 70. Available at: http://www.biomedcentral.com/1471-2229/11/70.
- Eulgem, T., Rushton, P.J., Robatzek, S., and Somssich, I.E. (2000). The WRKY superfamily of plant transcription factors. Trends Plant Sci. 5, 1360–1385.
- Gigon A.S., Matos, A.R., Laffray, D., Zuily-Fodil, Y., and Pham-Thi, A.T. (2004). Effect of Drought Stress on Lipid Metabolism in the Leaves of Arabidopsis thaliana (Ecotype Columbia). Ann. Bot. 94, 345–351.
- Gimeno, J., Gadea, J., Forment, J., Pérez-Valle, J., Santiago, J., Martínez-Godoy, M.A., Yenush, L., Bellés, J.M., Brumós, J., Colmenaro-Flores, J.M., Talón, M., and Serrano, R. (2009). Shared and novel molecular responses of mandarin to drought. Plant Mol. Biol. 70, 403–420.
- Hedley, P.E., Russel, J.R., Jorgensen, L., Gordon, S., Morris, J.A., Hackett, C.A., Cardle, L., and Brennan, R. (2010). Candidate genes associated with bud dormancy release in blackcurrant (Ribes nigrum L.). Plant Biol. 10, 202-215.
- Hsiao, T.C. (1973). Plant responses to water stress. Annu. Rev. Plant Biol. 24, 519–570.
- Huang, D., Wu, W., Abrams, S.R., and Cutler, A.J. (2008). The relationship of drought-related gene expression in Arabidopsis thaliana to hormonal and environmental factors. J. Exp. Bot. 59, 2991–3007.
- Jacoby, M., Weisshaar, B., Droge-Laser, W., Vicente-Carbajosa, J., Tiedemann, J., Kroj, T., Parcy, F., and bzip Research Group (2002). BZIP transcription factors in Arabidopsis. Trends Plant Sci. 7, 106–111.
- Jewell, M.C., Campbell, B.C., and Godwin, I.D. (2010). Transgenic Plants for Abiotic Stress Resistance. In Transgenic Crop Plants Volume 2; Utilisation and Biosafety, C. Kole, A.G. Michler, A.G. Abbott and T.C. Hail, eds. (Berlin, Heidelberg: Springer Verlag) pp. 494.
- Kahu, K., Jänes, H., Luik, A., and Klaas, L. (2009). Yield and fruit quality of organically cultivated blackcurrant cultivars. Acta Agric. Scand. B Soil Plant Sci. 59, 63–69.
- Li, J., Jia, D., and Chen, X. (2001). HUA1, a regulator of stamen and carpel identities in Arabidopsis, codes for a nuclear RNA binding protein. Plant Cell 13, 2269–2281.
- Lorenz, W.W., Alba, R., Yu, Y.S., Bordeaux, J.M., Simões, M., and Dean, J.F. (2011). Microarray analysis and scale-free gene networks identify candidate regulators in drought-stressed roots of loblolly pine (P. taeda L.). BMC Genomics 12, 1–17.
- Magome, H., Yamaguchi, S., Hanada, A., Kamiya, Y., and Oda, K. (2004). Dwarf and delayed-flowering 1, a novel Arabidopsis
mutant deficient in gibberellin biosynthesis because of overexpression of a putative AP2 transcription factor. Plant J. 37, 720–729.
- Qiang, L., Yong, Z., and Shouyi, C. (2000). Plant protein kinase genes induced by drought, high salt and cold stresses. Chinese Sci.Bull. 45, 1154–1157.
- Russel, J., Hackett, C., Hedley, P., Liu, H., Milne, L., Bayer, M., Marshall, D., Jorgensen, L., Gordon, S., and Brennan, R. (2014). The use of Genotyping by Sequencing in blackcurrant (Ribes nigrum) – developing high-resolution linkage maps in species without reference genome sequences. Mol. Breed. 33, 835–849.
- Shaik, R., and Ramakrishna, W. (2013). Genes and Co-Expression Modules Common to Drought and Bacterial Stress Responses in Arabidopsis and Rice. PLoS ONE 8(10): e77261. doi:10.1371/journal.pone.0077261.
- Shinozaki, K., and Yamaguchi-Shinozaki, K. (2007). Gene networks involved in drought stress response and tolerance. J. Exp. Bot. 58, 221–227.
- Slonim, D.K., and Yanai, I. (2009). Getting started in gene expression microarray analysis. PLoS Comput. Biol. 5, 1–4.
- Swindell, W.R., Huebner, M., and Weber, A.P. (2007). Transcriptional profiling of Arabidopsis heat shock proteins and transcription factors reveals extensive overlap between heat and non-heat stress response pathways. BMC Genomics 8, 125. doi:10.1186/1471-2164-8-125.
- Timperio, A.M., Egidi, M.G., and Zolla, L. (2008). Proteomics applied on plant abiotic stresses: Role of heat shock proteins (HSP). J. Proteomics 71, 391–411.
- Upchurch, R.G. (2008). Fatty acid unsaturation, mobilization, and regulation in the response of plants to stress. Biotechnol. Lett. 30, 967–977.
- Wang, W., Vinocur, B., and Altman, A. (2003). Plant responses to drought, salinity and extreme temperatures: towards genetic engineering for stress tolerance. Planta 218, 1–14.
- Wisniewski, M., Bassett, C., Norelli, J., Macarasin, D., Artlip, T., Gasic, K., and Korban, S. (2008). Expressed sequence tag analysis of the response of apple (Malus × domestica ‘Royal Gala’) to low temperature and water deficit. Physiol. Plant. 133, 298–317.
- Yan, D.H., Fenning, T., Tang, S., Xia, X., and Yin, W. (2012). Genomewide transcriptional response of Populus euphratica to long-term drought stress. Plant Sci. 195, 24–35.
- Zhang, J.Z. (2003). Overexpression analysis of plant transcription factors. Curr. Opin. Plant Biol. 6, 430–440.
- Zhou, X.F., Jin, Y.H., Yoo, C.Y., Lin, X.L., Kim, W.Y., Yun, D.J., Bressan, R.A., Haseqava, P.M., and Jin, J.B. (2013). CYCLIN H;1 regulates drought stress responses and blue light-induced stomatal opening by inhibiting reactive oxygen species accumulation in Arabidopsis. Plant Physiol. 162, 1030–1041.
- Zhu, J.K. (2001). Cell signaling under salt, water and cold stresses. Curr. Opin. Plant Biol. 4, 401–406.
Received: 16 July 2014 | Accepted: 18 November 2014 | Published: 26 February 2015 | Available online: 26 February 2015