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Selection for improved energy use efficiency and drought tolerance in canola results in distinct transcriptome and epigenome changes

Aurine Verkest (UGent) , Marina Byzova (UGent) , Cindy Martens (UGent) , Patrick Willems (UGent) , Tom Verwulgen (UGent) , Bram Slabbinck (UGent) , Debbie Rombaut (UGent) , Jan Van de Velde (UGent) , Klaas Vandepoele (UGent) , Evi Standaert, et al.
(2015) PLANT PHYSIOLOGY. 168(4). p.1338-1350
Author
Organization
Project
Biotechnology for a sustainable economy (Bio-Economy)
Project
Bioinformatics: from nucleotids to networks (N2N)
Abstract
To increase both the yield potential and stability of crops, integrated breeding strategies are used that have mostly a direct genetic basis, but the utility of epigenetics to improve complex traits is unclear. A better understanding of the status of the epigenome and its contribution to agronomic performance would help in developing approaches to incorporate the epigenetic component of complex traits into breeding programs. Starting from isogenic canola (Brassica napus) lines, epilines were generated by selecting, repeatedly for three generations, for increased energy use efficiency and drought tolerance. These epilines had an enhanced energy use efficiency, drought tolerance, and nitrogen use efficiency. Transcriptome analysis of the epilines and a line selected for its energy use efficiency solely revealed common differentially expressed genes related to the onset of stress tolerance-regulating signaling events. Genes related to responses to salt, osmotic, abscisic acid, and drought treatments were specifically differentially expressed in the drought-tolerant epilines. The status of the epigenome, scored as differential trimethylation of lysine-4 of histone 3, further supported the phenotype by targeting drought-responsive genes and facilitating the transcription of the differentially expressed genes. From these results, we conclude that the canola epigenome can be shaped by selection to increase energy use efficiency and stress tolerance. Hence, these findings warrant the further development of strategies to incorporate epigenetics into breeding.
Keywords
H3 LYSINE 4, MODEL DATA-ANALYSIS, ARABIDOPSIS-THALIANA, HISTONE H3, GENE-EXPRESSION, ABSCISIC-ACID, EPIGENETIC MUTATION, OSMOTIC-STRESS, PROBE LEVEL DATA, SEQUENCE-ANALYSIS

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Chicago
Verkest, Aurine, Marina Byzova, Cindy Martens, Patrick Willems, Tom Verwulgen, Bram Slabbinck, Debbie Rombaut, et al. 2015. “Selection for Improved Energy Use Efficiency and Drought Tolerance in Canola Results in Distinct Transcriptome and Epigenome Changes.” Plant Physiology 168 (4): 1338–1350.
APA
Verkest, A., Byzova, M., Martens, C., Willems, P., Verwulgen, T., Slabbinck, B., Rombaut, D., et al. (2015). Selection for improved energy use efficiency and drought tolerance in canola results in distinct transcriptome and epigenome changes. PLANT PHYSIOLOGY, 168(4), 1338–1350.
Vancouver
1.
Verkest A, Byzova M, Martens C, Willems P, Verwulgen T, Slabbinck B, et al. Selection for improved energy use efficiency and drought tolerance in canola results in distinct transcriptome and epigenome changes. PLANT PHYSIOLOGY. 2015;168(4):1338–50.
MLA
Verkest, Aurine, Marina Byzova, Cindy Martens, et al. “Selection for Improved Energy Use Efficiency and Drought Tolerance in Canola Results in Distinct Transcriptome and Epigenome Changes.” PLANT PHYSIOLOGY 168.4 (2015): 1338–1350. Print.
@article{6929884,
  abstract     = {To increase both the yield potential and stability of crops, integrated breeding strategies are used that have mostly a direct genetic basis, but the utility of epigenetics to improve complex traits is unclear. A better understanding of the status of the epigenome and its contribution to agronomic performance would help in developing approaches to incorporate the epigenetic component of complex traits into breeding programs. Starting from isogenic canola (Brassica napus) lines, epilines were generated by selecting, repeatedly for three generations, for increased energy use efficiency and drought tolerance. These epilines had an enhanced energy use efficiency, drought tolerance, and nitrogen use efficiency. Transcriptome analysis of the epilines and a line selected for its energy use efficiency solely revealed common differentially expressed genes related to the onset of stress tolerance-regulating signaling events. Genes related to responses to salt, osmotic, abscisic acid, and drought treatments were specifically differentially expressed in the drought-tolerant epilines. The status of the epigenome, scored as differential trimethylation of lysine-4 of histone 3, further supported the phenotype by targeting drought-responsive genes and facilitating the transcription of the differentially expressed genes. From these results, we conclude that the canola epigenome can be shaped by selection to increase energy use efficiency and stress tolerance. Hence, these findings warrant the further development of strategies to incorporate epigenetics into breeding.},
  author       = {Verkest, Aurine and Byzova, Marina and Martens, Cindy and Willems, Patrick and Verwulgen, Tom and Slabbinck, Bram and Rombaut, Debbie and Van de Velde, Jan and Vandepoele, Klaas and Standaert, Evi and Peeters, Marrit and Van Lijsebettens, Maria and Van Breusegem, Frank and De Block, Marc},
  issn         = {0032-0889},
  journal      = {PLANT PHYSIOLOGY},
  keyword      = {H3 LYSINE 4,MODEL DATA-ANALYSIS,ARABIDOPSIS-THALIANA,HISTONE H3,GENE-EXPRESSION,ABSCISIC-ACID,EPIGENETIC MUTATION,OSMOTIC-STRESS,PROBE LEVEL DATA,SEQUENCE-ANALYSIS},
  language     = {eng},
  number       = {4},
  pages        = {1338--1350},
  title        = {Selection for improved energy use efficiency and drought tolerance in canola results in distinct transcriptome and epigenome changes},
  url          = {http://dx.doi.org/10.1104/pp.15.00155},
  volume       = {168},
  year         = {2015},
}

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