title: Selection for Improved Energy Use Efficiency and Drought Tolerance in Canola Results in Distinct Transcriptome and Epigenome Changes.
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.
authors.affiliation: 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.).
authors.forename: Aurine
authors.identifier: http://orcid.org/0000-0003-3683-8537
authors.initials: A
authors.lastname: Verkest
authors.affiliation: 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.).
authors.forename: Marina
authors.identifier: http://orcid.org/0000-0001-8445-9377
authors.initials: M
authors.lastname: Byzova
authors.affiliation: 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.).
authors.forename: Cindy
authors.initials: C
authors.lastname: Martens
authors.affiliation: 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.).
authors.forename: Patrick
authors.identifier: http://orcid.org/0000-0003-4667-2294
authors.initials: P
authors.lastname: Willems
authors.affiliation: 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.).
authors.forename: Tom
authors.initials: T
authors.lastname: Verwulgen
authors.affiliation: 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.).
authors.forename: Bram
authors.initials: B
authors.lastname: Slabbinck
authors.affiliation: 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.).
authors.forename: Debbie
authors.initials: D
authors.lastname: Rombaut
authors.affiliation: 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.).
authors.forename: Jan
authors.initials: J
authors.lastname: Van de Velde
authors.affiliation: 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.).
authors.forename: Klaas
authors.identifier: http://orcid.org/0000-0003-4790-2725
authors.initials: K
authors.lastname: Vandepoele
authors.affiliation: 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.).
authors.forename: Evi
authors.initials: E
authors.lastname: Standaert
authors.affiliation: 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.).
authors.forename: Marrit
authors.initials: M
authors.lastname: Peeters
authors.affiliation: 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.).
authors.forename: Mieke
authors.identifier: http://orcid.org/0000-0002-7632-1463
authors.initials: M
authors.lastname: Van Lijsebettens
authors.affiliation: 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.
authors.forename: Frank
authors.identifier: http://orcid.org/0000-0002-3147-0860
authors.initials: F
authors.lastname: Van Breusegem
authors.affiliation: 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.
authors.forename: Marc
authors.identifier: http://orcid.org/0000-0003-0206-3825
authors.initials: M
authors.lastname: De Block
mesh_terms: D000040:Abscisic Acid / Q000378:metabolism*; D029688:Brassica napus / Q000235:genetics* / Q000502:physiology; D001947:Breeding; D018556:Crops, Agricultural; D055864:Droughts; D004734:Energy Metabolism; D044127:Epigenesis, Genetic; D057890:Epigenomics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D009995:Osmosis; D010641:Phenotype; D010937:Plant Growth Regulators / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D013312:Stress, Physiological; D059467:Transcriptome
chemical_list: D010937:Plant Growth Regulators; D000040:Abscisic Acid