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Phylogenetic Relationships, Marker Analysis, and Investigation of Genes Christian-Albrechts-Universität zu Kiel Promotionsordnung Agrar- u. Ernährungswiss. Fakultät 2020 Aus dem Institut für Landwirtschaftliche Verfahrenstechnik der Christian-Albrechts-Universität zu Kiel Phylogenetic relationships, marker analysis, and investigation of genes mediating high and low methyl salicylate biosynthesis in different birch species (Betula L., Betulaceae) Dissertation zur Erlangung des Doktorgrades der Agrar- und Ernährungswissenschaftlichen Fakultät der Christian-Albrechts-Universität zu Kiel vorgelegt von M. Sc. Kiran Singewar aus Nanded, Maharshtra, Indien Kiel, 2020 Dekan: Prof. Dr. Karl H. Mühling 1. Berichterstatter: Prof. Dr. Eberhart Hartung 2. Berichterstatter: PD. Dr. Matthias Fladung Tag der mündlichen Prüfung: 17th February 2021 Table of Contents 1. General introduction ........................................................................................................................ 1 1.1 Birch- its importance, morphology, and genetic architecture ........................................ 1 1.2 Birch- taxonomy and phylogenetic analysis .................................................................... 2 1.3 Methyl salicylate (MeSA) in plants ................................................................................. 4 1.4 Research issues and objectives .......................................................................................... 7 1.5 Scientific approach ............................................................................................................. 9 2. Species determination and phylogenetic relationships of the genus Betula inferred from multiple chloroplast and nuclear regions reveal the high methyl salicylate-producing ability of the ancestor ............................................................................................................................................... 10 2.1 Key message .................................................................................................................... 10 2.2 Abstract ..................................................................................................................... 11(1131) 2.3 Introduction ............................................................................................................... 11(1131) 2.4 Materials and methods ............................................................................................. 13(1133) 2.5 Results ....................................................................................................................... 15(1135) 2.6 Discussion ................................................................................................................. 18(1138) 2.7 Conclusion ................................................................................................................ 23(1143) 2.8 Future perspectives ................................................................................................... 24(1144) 2.9 Acknowledgment ...................................................................................................... 24(1144) 2.10 References ............................................................................................................... 24(1144) 3. Identification and analysis of key genes involved in methyl salicylate biosynthesis in different birch species ....................................................................................................................................... 27 3.1 Key message .................................................................................................................... 27 3.2 Abstract ..................................................................................................................... 28(1/24) 3.3 Introduction ............................................................................................................... 28(1/24) 3.4 Materials and methods ............................................................................................. 30(3/24) 3.5 Results ....................................................................................................................... 32(5/24) 3.6 Discussion ................................................................................................................ 40(13/24) 3.7 Acknowledgment ..................................................................................................... 46(19/24) 3.8 References ................................................................................................................ 47(20/24) 4. Genome-wide bioinformatics and phylogenetic analysis revealed putative substrate specificities of SABATH and MES family members in silver birch (Betula pendula) ................. 52 4.1 Key message .................................................................................................................... 52 4.2 Abstract ............................................................................................................................ 53 4.3 Introduction ...................................................................................................................... 54 4.4 Materials and methods .................................................................................................... 57 4.5 Results .............................................................................................................................. 59 4.6 Discussion ........................................................................................................................ 74 4.7 Conclusion ....................................................................................................................... 79 4.8 Acknowledgment ............................................................................................................. 80 4.9 Supplementary material .................................................................................................. 80 4.10 References ...................................................................................................................... 81 5. General discussion .......................................................................................................................... 85 5.1 Phylogenetic investigations in different birch species revealed the high MeSA producing ability of the ancestor .......................................................................................... 85 5.2 Candidate gene, marker, and tissue-specific expression analysis in different birches 86 5.3 Evolutionary relationships and putative substrate specificities of SABATH and MES enzyme family members of silver birch ............................................................................... 87 6. Conclusions .................................................................................................................................... 89 7. Summary ......................................................................................................................................... 90 8. Zusammenfassung........................................................................................................................... 92 9. References ...................................................................................................................................... 95 10. Declaration of co-authorship ....................................................................................................... 99 11. Acknowledgements .................................................................................................................... 103 1 General introduction 1.1 Birch- its importance, morphology, and genetic architecture The Northern Hemisphere incorporates around 30% of the global forest area and contains highly dense trees that maintain the global forest ecosystem (Crowther et al., 2015; Gauthier et al., 2015). The most common genera distributed in the region is Alnus (Alders), Betula (Birches), Carpinus (Hornbeams), Corylus (Iron-wood), Ostrya (Hazel), and Ostryopsis (Hazel-hornbeam) all belonging to the Betulaceae family (Chen et al., 1999; Rastogi et al., 2015; Christenhusz et al., 2016). The family is distributed in Europe, the Caucasus, and Asia (Chen, 1994; Shaw et al., 2015). The genus Betula is the largest group of dominant trees and shrubs of the Betulaceae family, found in the Northern Hemisphere (Rastogi et al., 2015; Shaw et al., 2015). They diverged from the sister genera of the Betulaceae family around 75 million years ago (Bina et al., 2016). The number of Betula species in the genus extends from 30 to 120 (Furlow, 1990; Koropachinskii, 2013) and some new species have also been described lately (Zeng et al., 2008; McAllister et al., 2011). Birches are considered ecologically significant plants that play an important role in forestry and horticulture (Ashburner et al., 2013). They are fertile seed producers, light- demanding pioneer species, able to grow within a short time, and the foremost species, even after forest fire, to show juvenile growth (Fischer et al., 2002). The potential of renewable energy and biomass production from birch with economic benefits has been successful in Europe (Hynynen et al., 2009). Additionally, the breeding of birch for the rapid development and income-generating commercial plantations has been a traditional activity in many European countries (Stener et al., 2005; Gailis et al., 2020). Several species of the genus Betula, including Betula pendula and Betula pubescens,
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