Schriftenreihe des Instituts für Tierzucht und Tierhaltung der Christian-Albrechts-Universität zu Kiel, Heft 225, 2019 ©2019 Selbstverlag des Instituts für Tierzucht und Tierhaltung der Christian-Albrechts-Universität zu Kiel Olshausenstraße 40, 24098 Kiel Schriftleitung: Prof. Dr. J. Krieter ISSN: 0720-4272 Gedruckt mit Genehmigung des Dekans der Agrar- und Ernährungswissen- schaftlichen Fakultät der Christian-Albrechts-Universität zu Kiel Aus dem Institut für Tierzucht und Tierhaltung der Agrar- und Ernährungswissenschaftlichen Fakultät der Christian-Albrechts-Universität zu Kiel ___________________________________________________________________________ Conservation Genetics and Management of Local Breeds DISSERTATION zur Erlangung des Doktorgrades Doctor scientiarum agrariarum (Dr. sc. agr.) der Agrar- und Ernährungswissenschaftlichen Fakultät der Christian-Albrechts-Universität zu Kiel vorgelegt von M.Sc. Jonas Schäler aus Potsdam Brandenburg Kiel, 2018 Dekan: Prof. Dr. Dr. Christian Henning 1. Berichterstatter: Prof. Dr. Georg Thaller 2. Berichterstatter: Prof. Dr. Dirk Hinrichs Tag der mündlichen Prüfung: 23.01.2019 ___________________________________________________________________________ Die Dissertation wurde mit dankenswerter Unterstützung des Ministeriums für Energie, Landwirtschaft, Umwelt, Natur und Digitalisierung im Rahmen der Europäischen Innovationsförderungspartnerschaft (EIP Agri) angefertigt. Table of Contents __________________________________________________________________________________________ Table of Contents General Introduction…………………….…………………………………………………………………..1 Chapter One Comparison of ancestral, partial, and genomic inbreeding in a local pig breed to achieve genetic diversity…………………………………………………………...………………………....5 Chapter Two Performance of a novel breeding value in context of breed conservation…...................................29 Chapter Three Genetic diversity and historic introgression in German Angler and Red Dual Purpose cattle and possibilities to reverse introgression…………..………………..…...37 Chapter Four The benefit of native genetic contribution in a local cattle breed……………………......................59 Chapter Five Implementation of breed-specific traits for a local sheep breed…………………………….............73 Chapter Six Exploration of conservation and development strategies for local cattle breeds in Northern Germany………………………………………………………………………………..……….97 General Discussion………………..............................................................................................................123 General Summary………………………………..………………….………………………...…………..141 Allgemeine Zusammenfassung………………………………………………………………………...143 General Introduction __________________________________________________________________________________________ General Introduction An impressive variety of breeds emerged since the domestication of livestock species due to a long history of migrations, selection, and adaptation (Groeneveld et al. 2010). Many well- defined breeds are utilized nowadays for a broad range of purposes and express distinct performance levels depending on specific local environments. Only few specialized and high- yielding breeds dominate the commercial sector, but still many local breeds can be found mostly for socioeconomic reasons (Tisdell 2003). However, advanced technology and efficient breeding programs further reduce the competitiveness of those local breeds. As a consequence, high-yielding breeds increasingly replace local breeds (Meuwissen 2009) causing negative impact on population genetic properties of local breeds (FAO 2010; Wang et al. 2017). Population sizes of numerous local breeds already decreased dramatically and some of them are threatened by extinction (Fernández et al. 2011). Conservation of genetic diversity is therefore of major importance (Frankham 1995; Caballero and Toro 2002) and there is international agree to maintain breeds and their genetic diversity as a unique genetic resource for the future (Boettcher et al. 2010). In general, the genetic diversity of local populations is impacted by small effective population sizes and lack of pedigree recording which in addition enforces inbreeding. With this respect, Chapter One deals with the estimation of relatedness and different inbreeding measurements based on pedigree and on the genomic level for a small local pig breed in Northern Germany. Furthermore, correlations between inbreeding estimators were investigated. Another aspect is the fact that genetic material from high-yielding breeds has been introgressed into local breeds for decades in order to increase genetic gain and enhance profitability. As a consequence, genetic diversity per se increased whereas native genetic diversity decreased in populations. Therefore, an appropriate instrument was developed in Chapter Two, which enables to select on native genetic contribution (NC) and thus, increase native genetic diversity demonstrated for two local cattle breeds, the German Angler and the Red Dual-Purpose cattle. The - 1 - General Introduction __________________________________________________________________________________________ population parameter of NC was considered as a trait and its genetic parameters were estimated with different linear mixed models. To find a balance between genetic gain, inbreeding, and the enhancement of NC or native uniqueness the advanced Optimum Contribution Selection (OCS) accounting for historic introgression from Wellmann et al. (2012) was applied for the two local cattle breeds in Chapter Three. Thereby, results for genetic gain of the conventional advanced OCS and of modified OCS scenarios, in which NC was included as a trait rather than a constraint, were compared in order to recover the native genetic background. In addition, population genetic parameters for both breeds were identified over the last generations. To date, there is no scientific justification for the utility of achieving NC or native genetic diversity within single breeds. In Chapter Four NC was used as a trait to prove correlations between NC and major traits on genomic level. Conventional breeding programs and intense management may cause negative effects regarding maintenance of special characteristics of local breeds. Chapter Five describes an approach how to identify and evaluate breed-specific characteristics for a typical environment in contrast to performance testing on station for a local sheep breed. Another important part beside conservation genetics is the aspect of breed management to maintain and support local breeds as far as possible. In Chapter Six a combination of qualitative and quantitative decision tools was adapted to identify strengths, weaknesses, opportunities, and threats. The output was transferred to the primary level in order to form the most objective conservation and development strategies for the two local cattle breeds. REFERENCES Boettcher PJ, Tixier-Boichard M, Toro MA, Simianer H, Eding H, Gandini G, Joost S, Garcia D, Colli L, Ajmone-Marsan P, The GLOBALDIV Consortium (2010) Objectives, criteria and methods for using molecular genetic data in priority setting for conservation of animal genetic resources. Animal Genetics 41(1):64-77 - 2 - General Introduction __________________________________________________________________________________________ Caballero A, Toro MA (2002) Analysis of genetic diversity for the management of conserved subdivided populations. Conservation Genetics 3:289-299 FAO (2010) Breeding strategies for sustainable management of animal genetic resources. FAO Animal Production and Health Guidelines. No. 3, Rome Fernández J, Meuwissen THE, Toro MA, Mäki-Tanila A (2011) Management of genetic diversity in small farm animal populations. Animal 5(11):1684-1698 Frankham R (1995) Conservation genetics. Annual Review of Genetics 29:305-327 Groeneveld LF, Lenstra JA, Eding H, Toro MA, Scherf B, Pilling D, Negrini R, Finlay EK, Jianlin H, Groeneveld E, Weigend S, The GLOBALDIV Consortium (2010) Genetic diversity in farm animals – a review. Animal Genetics 41(1):6-31 Meuwissen THE (2009) Genetic management of small populations: A review. Acta Agriculturae Scandinavica, Section A – Animal Science 59(2):71-79 Tisdell C (2003) Socioeconomic causes of loss of animal genetic diversity: analysis and assessment. Ecological Economics 45:365-376 Wang Y, Bennewitz J, Wellmann R (2017) Novel optimum contribution selection methods accounting for conflicting objectives in breeding programs for livestock breeds with historical migration. Genetics Selection Evolution 49:45 Wellmann R, Hartwig S, Bennewitz J (2012) Optimum contribution selection for conserved populations with historic migration. Genetics Selection Evolution 44(1):34 - 3 - Chapter One __________________________________________________________________________________________ Chapter One Comparison of ancestral, partial, and genomic inbreeding in a local pig breed to achieve genetic diversity J. Schäler1, B. Krüger2, G. Thaller1 & D. Hinrichs3 1Institute of Animal Breeding and Husbandry, Christian-Albrechts-University, Hermann- Rodewald-Straße 6, 24098 Kiel, Germany 2Institute of Zoology, Christian-Albrechts-University, Am Botanischen Garten 1-9, 24118 Kiel, Germany 3Faculty of Organic Agricultural Sciences, Department of Animal Breeding, University of Kassel, Nordbahnhofstraße 1a, 37213 Witzenhausen, Germany Published in Conservation Genetics Resources (in press) - 5 - Chapter One __________________________________________________________________________________________