FACULTY OF AGRICULTURE Maja Ferenčaković Molecular dissection of inbreeding depression for semen quality traits in cattle DOCTORAL THESIS Zagreb, 2015 AGRONOMSKI FAKULTET Maja Ferenčaković Molekularna disekcija inbriding depresije za svojstva kvalitete sperme kod goveda DOKTORSKI RAD Zagreb, 2015. FACULTY OF AGRICULTURE Maja Ferenčaković Molecular dissection of inbreeding depression for semen quality traits in cattle DOCTORAL THESIS Supervisors: Professor Ino Čurik, PhD Professor Johann Sölkner, PhD Zagreb, 2015 AGRONOMSKI FAKULTET Maja Ferenčaković Molekularna disekcija inbriding depresije za svojstva kvalitete sperme kod goveda DOKTORSKI RAD Mentori: prof. dr. sc. Ino Čurik Univ. Prof. DI. Dr. Johann Sölkner Zagreb, 2015. Supervisors: prof. dr. sc. Ino Čurik Department of Animal Science Faculty of Agriculture, University of Zagreb Svetošimunska cesta 25, 10000 Zagreb, Croatia [email protected] Univ. Prof. DI. Dr. Johann Sölkner University of Natural Resources and Life Sciences, Vienna, Austria [email protected] This doctoral thesis was evaluated by the Dissertation Evaluation Committee members: 1. Miroslav Kapš, PhD Full professor, Faculty of Agriculture, University of Zagreb, Croatia 2. Johannes Arjen Lenstra, PhD Associate professor, Utrecht University, Institute for Risk Assessment Sciences, The Netherlands 3. Vlatka Čubrić Čurik, PhD Assistant professor, Faculty of Agriculture, University of Zagreb, Croatia Doctoral thesis was defended at Faculty of Agriculture, University of Zagreb on ____________ 2015 in front of the Dissertation Defense Committee members: 1. Miroslav Kapš, PhD, _______________ Full professor, Faculty of Agriculture, University of Zagreb, Croatia, 2. Johannes Arjen Lenstra, PhD, _______________ Associate professor, Utrecht University, Institute for Risk Assessment Sciences, The Netherlands, 3. Vlatka Čubrić Čurik, PhD, _______________ Assistant professor, Faculty of Agriculture, University of Zagreb, Croatia. Acknowledgements First of all, I would like to thank my mentor prof. dr. sc. Ino Čurik who guided me through the process of becoming a scientist in every sense of the word. I am grateful for your leadership, support, selflessly sharing knowledge, motivation and encouraging me to simply follow where the data lead. You helped with my personal and academic development. I cannot think of a better mentor to have. Truly, there are no words that could express my deep gratitude to you. Many thanks to Univ. Prof. DI. Dr. Johann Sölkner for patience, encouragement and all the time dedicated to guide me in research. Thank you for giving me opportunity to work with you and for all your advices and encouragements in tough times. I would like to express my deepest gratitude to doc. dr. sc. Vlatka Čubrić Čurik for support, caring for my future and for constantly reminding me that I have to finish my Ph.D. Thank you for being a good friend and excellent motivator. Big thanks to prof. dr. sc. Miroslav Kapš for honest and unselfish support, sharing knowledge about modeling and all the help with solving statistical issues encountered during writhing this Thesis. You have provided invaluable perspectives on my research when most needed I take this opportunity to express my gratitude to Dr. Johannes Lenstra for the useful comments and engagement through the process of writing of this thesis. Thank you for always finding time to propose consistently excellent improvements. For funding I would like to acknowledge the Croatian Ministry of Science, Education and Sports (project 178-1780460-0546, ‘Strategies for elimination of genetic defects in selected populations’), by a bilateral collaborative project involving the Croatian Ministry of Science, Education and Sports and the Austrian Agency for International Cooperation in Education and Research (OeADGmbH) (“Analysis of genetic diversity in cattle populations using dense sets of molecular markers”),“Ernst Mach grant – worldwide” financed by the Austrian Federal Ministry of Education and Science, Erasmus Mundus programme ‘European Master in animal Breeding and Genetics’, financed by the European Commission and European Science Foundation networking program “Advances in Farm Animal Genomic Resources” (“GENOMIC- RESOURCES”) grant (EX/3733) for which I am deeply thankful. I am very grateful to Zuchtdata EDV-Dienstleistungen GmbH and Geno SA, as well as Austrian Simmental association and Braunvieh Austria, Association of the Tyrolian Grey Cattle Breeders, Austrian association of the Pinzgauer cattle breeders and Federation of Austrian Cattle Breeders for provision of genotype and pedigree data. I would like to thank Dipl. Ing. Peter Stückler from Besamungsanstalt Gleisdorf, Dr. Josef Miesenberger from Besamungsanstalt Hohenzell and Dr. Friedrich Führer from NÖ-Genetik Wieselburg for provision of semen quality records. I would specially like to thank Golden Helix team for providing me free license for SNP & Variation Suite v7.6.8 Win64, which allowed me easy, efficient and headache- free work with genotype data. Thank you for making process of data preparation enjoyable experience. Many thanks to my friend Miroslav Horvacki who selflessly helped me to solve all those mysteries of installing and working with various strange software and platforms. This thesis would not have been possible to write without your help. A special mention for Dr. Félix Goyache; “Little by little…” was something I often heard from you and I continued practicing this philosophy permanently in my life. Thank you for lively discussions, encouraging emails, and sharing relevant publications. I would like to thank my colleagues from Department of Animal Science for support and friendship and being there when I needed help. To all my friends and dear people who patiently helped me to stay focused on my goal when I was exhausted and crazy and who kept reminding me there is a whole world outside of my PhD. Also, thank you for all your support, advice and belief that I was capable of taking on the PhD. To my brother and his family who always jumped in and helped every time there were things to do at home when I was abroad. Knowing that you are there brought me peace of mind and ability to easy concentrate to my work instead of worrying about all those domestic stuff, which are impossible to do if not present. Finally I would like to thank my mother who has supported me throughout the entire process and who was silently proud at all my achievements. I will be grateful forever. Thank you Preface This PhD thesis is based on four articles (Chapters 1, 3, 4 and 5), which are published in international journals, as well as study prepared for publication in which identification of genomic regions associated with inbreeding depression on semen quality traits is investigated (Chapter 5). A detailed literature review is presented in Chapter 1 in form of review article published in “Livestock Science” by Ino Čurik, Maja Ferenčaković and Johann Sölkner. Chapter 2 gives the hypotheses stated in this thesis and the resulting objectives. Chapter 3 was published in Journal of Animal Breeding & Genetics by Maja Ferenčaković, Edin Hamzić, Birgit Gredler, Trygve Solberg, Gunnar Klemetsdal, Ino Čurik and Johann Sölkner. This work is one of the first analyses of Runs of homozygosity (ROH) in cattle. It is important to notice that before this analysis similar studies were performed only in humans with exception of an EAAP conference paper in 2010 (Sölkner et al. 2010) and one paper published 2011, both by the same group of authors (article is in the supplementary material). This pioneer research was published in Agriculturae Conspectus Scientificus and this chapter is extension and confirmation of this research on larger sample and in more cattle populations. Chapter 4 was published in “Genetics Selection Evolution” by Maja Ferenčaković, Johann Sölkner and Ino Čurik. This article represents first comprehensive analysis of the issues that can arise in process of ROH determination and FROH. Chapter 5 present material and methods and results and discussion of unpublished part of this Thesis. This part shows how ROH approach can be used for estimating inbreeding depression. It clearly shows that simple attempt of finding regions that are responsible for changes in semen quality traits when they are autozygous, can yield in finding genes that are proven to affect fertility, as well as some whose function highly suggests important role for fertility traits. In Chapters 6 and 7 general discussion and conclusions are presented Copies of publications which I co-authored and which are directly associated with this Thesis are attached as Supplementary material A hundred times every day I remind myself that my inner and outer life depend on the labors of other men, living and dead, and that I must exert myself in order to give in the same measure as I have received and am still receiving. Albert Einstein, (1879 - 1955) ABSTRACT Runs Of Homozygosity (ROH) are a newly introduced approach for identifying inbreeding in diploid individuals. This approach is more reliable and available than pedigree data, but the lack of universal standards about ROH definition and identification introduces serious bias in ROH studies. In this thesis, ROH were analyzed in five cattle breeds (Brown Swiss, Fleckvieh, Norwegian Red, Pinzgauer and Tyrol Grey). The effects of SNP chip density and genotyping errors were tested on Brown Swiss, Pinzgauer and Tyrol Grey in order to establish the most optimal settings for precise estimation of levels of autozygosity.