Selection for Improved Energy Use Efficiency and Drought Tolerance in Canola Results in Distinct Transcriptome and Epigenome Changes

Aurine Verkest; Marina Byzova; Cindy Martens; Patrick Willems; Tom Verwulgen; Bram Slabbinck; Debbie Rombaut; Jan Van de Velde; Klaas Vandepoele; Evi Standaert; Marrit Peeters; Mieke Van Lijsebettens; Frank Van Breusegem; Marc De Block

doi:10.1104/pp.15.00155

Selection for Improved Energy Use Efficiency and Drought Tolerance in Canola Results in Distinct Transcriptome and Epigenome Changes

Plant Physiol. 2015 Aug;168(4):1338-50. doi: 10.1104/pp.15.00155. Epub 2015 Jun 16.

Affiliations

¹ Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (A.V., M.B., C.M., P.W., T.V., B.S., D.R., J.V.d.V., K.V., M.V.L., F.V.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (A.V., M.B., C.M., P.W., T.V., B.S., D.R., J.V.d.V., K.V., M.V.L., F.V.B.);Bayer CropScience, 9052 Ghent, Belgium (C.M., E.S., M.P., M.D.B.);Department of Medical Protein Research, VIB, 9000 Ghent, Belgium (P.W.); andDepartment of Biochemistry, Ghent University, 9000 Ghent, Belgium (P.W.).
² Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium (A.V., M.B., C.M., P.W., T.V., B.S., D.R., J.V.d.V., K.V., M.V.L., F.V.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (A.V., M.B., C.M., P.W., T.V., B.S., D.R., J.V.d.V., K.V., M.V.L., F.V.B.);Bayer CropScience, 9052 Ghent, Belgium (C.M., E.S., M.P., M.D.B.);Department of Medical Protein Research, VIB, 9000 Ghent, Belgium (P.W.); andDepartment of Biochemistry, Ghent University, 9000 Ghent, Belgium (P.W.) frank.vanbreusegem@psb.vib-ugent.be marc.deblock@bayer.com.

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Abscisic Acid / metabolism*
Brassica napus / genetics*
Brassica napus / physiology
Breeding
Crops, Agricultural
Droughts
Energy Metabolism
Epigenesis, Genetic*
Epigenomics
Gene Expression Profiling
Gene Expression Regulation, Plant
Osmosis
Phenotype
Plant Growth Regulators / metabolism*
Sequence Analysis, RNA
Stress, Physiological
Transcriptome*

Substances

Plant Growth Regulators
Abscisic Acid

Associated data

GEO/GSE65578