MARIA HELENE PALESA JAEGER Phenotypic, Quantitative Genetic and Genomic Characterization of the German Black and White Dual-Purpose Cattle Breed Genetic Studies on Black and White Cattle INAUGURAL-DISSERTATION édition scientifique zur Erlangung des Doktorgrades eines Doctor agriculturae (Dr. agr.) VVB LAUFERSWEILER VERLAG durch den Fachbereich Agrarwissenschaften, Ökotrophologie und VVB LAUFERSWEILER VERLAG STAUFENBERGRING 15 ISBN: 978-3-8359-6754-0 Umweltmanagement der Justus-Liebig-Universität Gießen D-35396 GIESSEN VVB Maria Helene Palesa Jaeger Tel: 0641-5599888 Fax: -5599890 [email protected] www.doktorverlag.de 9 7 8 3 8 3 5 9 6 7 5 4 0 VVB édition scientifique VERLAG VVB LAUFERSWEILER VERLAG Photo cover: © Aus dem Institut für Tierzucht und Haustiergenetik Professur für Tierzüchtung der Justus-Liebig-Universität Gießen __________________________________________________________________ Phenotypic, Quantitative Genetic and Genomic Characterization of the German Black and White Dual- Purpose Cattle Breed INAUGURAL-DISSERTATION zur Erlangung des Doktorgrades (Dr. agr.) im Fachbereich Agrarwissenschaften, Ökotrophologie und Umweltmanagement der Justus-Liebig-Universität Gießen vorgelegt von MARIA HELENE PALESA JAEGER aus Roma, Lesotho Gießen, 5. Oktober 2018 Mit Genehmigung des Fachbereiches Agrarwissenschaften, Ökotrophologie und Umweltmanagement der Justus-Liebig-Universität Gießen Dekan: Prof. Dr. Klaus Eder Prüfungskommission 1. GUTACHTER: Prof. Dr. Sven König 2. GUTACHTER: Prof. Dr. Dirk Hinrichs Prüfer: Prof. Dr. Andreas Gattinger Prüfer: Prof. Dr. Horst Brandt Vorsitzender: Prof. Dr. Rod Snowdon Tag der Disputation 13. Dezember 2018 The key is a man’s power of accumulative selection: nature gives successive variations; man adds them up in certain directions useful to him. Charles Darwin Meiner Familie Table of Contents LIST OF TABLES ......................................................................................................... IV LIST OF FIGURES ........................................................................................................ VI LIST OF ABBREVIATIONS ...................................................................................... VIII SUMMARY ..................................................................................................................... 1 ZUSAMMENFASSUNG ................................................................................................. 8 CHAPTER 1 ................................................................................................................... 16 GENERAL INTRODUCTION ........................................................................................... 16 Changes in the dairy sector ..................................................................................... 17 Grassland systems and organic dairy production .................................................... 18 Situation of endangered native dual-purpose cattle breeds in Germany ................. 20 References ............................................................................................................... 25 CHAPTER 2 ................................................................................................................... 29 INBREEDING AND GENETIC RELATIONSHIPS OF THE ENDANGERED DUAL-PURPOSE BLACK AND WHITE CATTLE BREED BASED ON OWN GENETIC BREED PERCENTAGE CALCULATIONS ........................................................................................................... 29 Einleitung ................................................................................................................ 30 Material und Methoden ........................................................................................... 32 Ergebnisse ............................................................................................................... 37 Diskussion ............................................................................................................... 42 Schlussfolgerung ..................................................................................................... 47 Literatur ................................................................................................................... 49 CHAPTER 3 ................................................................................................................... 52 ASSOCIATIONS BETWEEN PRECISION SENSOR DATA WITH SUBJECTIVELY SCORED CATTLE WELFARE INDICATORS, TEST-DAY PRODUCTION-, HEALTH- AND I FERTILITY TRAITS IN NATIVE BLACK AND WHITE DUAL-PURPOSE CATTLE KEPT IN PASTURE-BASED PRODUCTION SYSTEMS ................................................................... 52 Introduction ............................................................................................................. 53 Materials and Methods ............................................................................................ 57 Results ..................................................................................................................... 60 Discussion ............................................................................................................... 64 Conclusion ............................................................................................................... 70 References ............................................................................................................... 71 CHAPTER 4 ................................................................................................................... 74 MULTI-BREED GWAS FOR ELECTRONICALLY RECORDED CATTLE BEHAVIOUR TRAITS ......................................................................................................................... 74 Introduction ............................................................................................................. 75 Materials and Methods ............................................................................................ 77 Results ..................................................................................................................... 84 Discussion ............................................................................................................... 95 Conclusion ............................................................................................................. 106 References ............................................................................................................. 108 CHAPTER 5 ................................................................................................................. 117 VARIANCE HETEROGENEITY AND GENOTYPE BY ENVIRONMENT INTERACTIONS IN NATIVE BLACK AND WHITE DUAL-PURPOSE CATTLE FOR DIFFERENT HERD ALLOCATION SCHEMES ............................................................................................ 117 Introduction ........................................................................................................... 118 Materials and Methods .......................................................................................... 120 Results ................................................................................................................... 124 Discussion ............................................................................................................. 134 Conclusion ............................................................................................................. 139 References ............................................................................................................. 140 II CHAPTER 6 ................................................................................................................. 144 SIMULATION AND ECONOMIC EVALUATION OF BLACK AND WHITE DUAL-PURPOSE CATTLE BREEDING PROGRAMS ................................................................................ 144 Introduction ........................................................................................................... 145 Materials and Methods .......................................................................................... 147 Results ................................................................................................................... 152 Discussion ............................................................................................................. 158 Conclusion ............................................................................................................. 163 References ............................................................................................................. 165 CHAPTER 7 ................................................................................................................. 169 GENERAL DISCUSSION .............................................................................................. 169 GENETIC ASSOCIATIONS BETWEEN PRODUCTIVITY AND COW BEHAVIOUR .......... 171 Introduction ........................................................................................................... 171 Materials and Methods .......................................................................................... 173 Results and Discussion .......................................................................................... 175 Conclusion ............................................................................................................. 181 FUTURE PERSPECTIVES ............................................................................................