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Onobrychis Viciifolia) Research Collection Doctoral Thesis Self-fertilization and marker-trait associations in sainfoin (Onobrychis viciifolia) Author(s): Kempf, Katharina Publication Date: 2016 Permanent Link: https://doi.org/10.3929/ethz-a-010852406 Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library DISS. ETH NO. 23568 SELF-FERTILIZATION AND MARKER-TRAIT ASSOCIATIONS IN SAINFOIN (ONOBRYCHIS VICIIFOLIA) A thesis submitted to attain the degree of DOCTOR OF SCIENCES of ETH ZURICH (Dr. sc. ETH Zurich) presented by KATHARINA KEMPF Dipl.-Agr.Biol., University of Hohenheim born on 17.04.1985 citizen of Germany accepted on the recommendation of Prof. Dr. Achim Walter, examiner Prof. Dr. Michael Kreuzer, co-examiner Prof. Dr. Bruno Studer, co-examiner Dr. Roland Kölliker, co-examiner 2016 Content List of Tables .............................................................................................................. v List of Figures ...................................................................................................... vii List of Abbreviations ................................................................................................. ix Summary .................................................................................................................... 1 Zusammenfassung ..................................................................................................... 5 Chapter 1: General Introduction ............................................................................... 9 1.1 Grassland production systems ....................................................................... 11 1.1.1 Importance of grassland........................................................................... 11 1.1.2 Use of legumes .......................................................................................... 12 1.2 Genetic improvement of plants: background information ............................ 13 1.2.1 Mating systems in plants ......................................................................... 13 1.2.2 Polyploidy in plants .................................................................................. 14 1.2.3 Breeding methods in forage plants .......................................................... 16 1.2.4 Genetic markers to assist plant breeding ............................................... 18 1.3 Sainfoin ........................................................................................................... 20 1.3.1 Taxonomy ................................................................................................. 20 1.3.2 Origin and historical distribution ............................................................ 21 1.4 Basic characteristics of sainfoin ..................................................................... 22 1.4.1 Morphology ............................................................................................... 22 1.4.2 Chemical properties of sainfoin ............................................................... 24 1.5 Cultivation and use ........................................................................................ 26 1.5.1 Nowadays distribution ............................................................................. 26 1.5.2 Cultivation ................................................................................................ 27 1.5.3 Usage ........................................................................................................ 29 1.6 Genetic improvement of sainfoin ................................................................... 30 1.6.1 Reproduction system ................................................................................ 30 1.6.2 Polyploidy ................................................................................................. 31 1.6.3 Breeding activities.................................................................................... 32 1.6.4 Breeding goals and genetic resources ...................................................... 33 1.7 Objectives of the thesis within the LegumePlus project ............................... 35 i Chapter 2: Evidence and consequences of self-fertilization in the predominantly outbreeding forage legume Onobrychis viciifolia .................................................. 37 2.1 Abstract .......................................................................................................... 38 2.2 Background..................................................................................................... 39 2.3 Methods .......................................................................................................... 42 2.3.1 Plant material and field trial .................................................................. 42 2.3.2 Phenotyping of ADP populations ............................................................ 43 2.3.3 DNA extraction and marker genotyping ................................................ 44 2.3.4 Detection of self-fertilization ................................................................... 46 2.3.5 Statistical analysis .................................................................................. 46 2.4 Results ............................................................................................................ 47 2.4.1 Self-fertilization in ADP populations ...................................................... 47 2.4.2 Self-fertilization in NDP populations ..................................................... 49 2.4.3 Phenotypic characterization of ADP populations ................................... 50 2.5 Discussion ....................................................................................................... 53 2.5.1 High rates of self-fertilization can be induced ........................................ 53 2.5.2 Power to detect selfings ........................................................................... 54 2.5.3 Inbreeding depression dependent on trait .............................................. 55 2.6 Conclusions ..................................................................................................... 57 2.7 Authors’ contributions ................................................................................... 58 2.8 Acknowledgments .......................................................................................... 58 2.9 Supplementary Information .......................................................................... 59 Chapter 3: Characterization of novel SSR markers in diverse sainfoin (Onobrychis viciifolia) germplasm ......................................................................... 63 3.1 Abstract .......................................................................................................... 64 3.2 Introduction .................................................................................................... 65 3.3 Material and Methods .................................................................................... 67 3.3.1 Plant material .......................................................................................... 67 3.3.2 DNA extraction ........................................................................................ 68 3.3.3 PCR and gel electrophoresis .................................................................... 68 3.3.4 M13 PCR capillary electrophoresis ......................................................... 69 3.3.5 Data analysis ........................................................................................... 72 3.4 Results ............................................................................................................ 73 3.4.1 SSR analysis ............................................................................................ 73 ii 3.4.2 Diversity of Onobrychis viciifolia individuals ......................................... 77 3.5 Discussion ....................................................................................................... 79 3.6 Conclusions ..................................................................................................... 82 3.7 Acknowledgments ........................................................................................... 83 3.8 Authors‘ contributions .................................................................................... 83 3.9 Supplementary Information ........................................................................... 84 Chapter 4: Marker-trait association analysis for agronomic and compositional traits in sainfoin (Onobrychis viciifolia) ................................................................. 87 4.1 Abstract ........................................................................................................... 88 4.2 Introduction .................................................................................................... 89 4.3 Material and Methods .................................................................................... 92 4.3.1 Plant material .......................................................................................... 92 4.3.2 Phenotyping .............................................................................................. 92 4.3.3 Genotyping................................................................................................ 94 4.3.4 Statistical
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