Exploring the complex population structure and admixture of four local Hungarian sheep breeds

Johanna Ramírez-Díaz ¹ Tania Bobbo ² Bernt Guldbrandtsen ³ Anna A. Schönherz ⁴ Paolo Cozzi ¹ Szilvia Kusza ^5* Goutam Sahana ⁶ Bertrand Servin ⁷ Alessandra Stella ^1* Arianna Manunza ¹

• ¹ Institute of Agricultural Biology and Biotechnology, National Research Council (CNR), Milan, Italy
• ² Institute of Biomedical Technologies, Department of Biomedical Sciences, National Research Council (CNR), Segrate, Lombardy, Italy
• ³ Novo Nordisk (Denmark), Copenhagen, Denmark
• ⁴ Department of Animal Science, Faculty of Technical Sciences, Aarhus University, Aarhus, Capital Region of Denmark, Denmark
• ⁵ Center for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Nyíregyháza, Hungary
• ⁶ Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Faculty of Natural Sciences, Aarhus University, Aarhus, Capital Region of Denmark, Denmark
• ⁷ GenPhySE, Université de Toulouse, INRAE, Toulouse, France

The origin of sheep and their spread after the emergence of domestication has been widely investigated using archaeology, genetics and genomics. A deep investigation of the genetic diversity of the breeds is key to provide useful information for the conservation and breeding programs. In Hungary, sheep farming contributes to the agricultural sector and national economy. It mostly plays a role in rural livelihoods, exports, and environmental management while also contributing to the national economy and preserving Hungary's cultural and agricultural heritage through traditional breeds. This study aims to analyse the population structure and patterns of admixture in four local Hungarian sheep breeds: Indigenous Tsigai, Hortobagyi Racka, Cikta and Bábolna Tetra. Our results revealed that the indigenous Hungarian Hortobagyi Racka sheep are distinct from the other Hungarian breeds under study. The effective population sizes are found to be low, with varying levels of genomic inbreeding both within and across breeds. These results align with documented bottlenecks and instances of crossbreeding with other local or improved breeds. Ancestry analysis demonstrated some introgression from Scandinavian into Hungarian sheep breeds and vice versa. This gene flow may have occurred recently due to the widespread use of northern breeds such as Finnsheep and Romanov to enhance productivity, but it could also be much older. Even with some limitations, our outcomes would be used to promote future conservation plans and a more comprehensive analysis of all native Hungarian sheep breeds should be highlighted to the relevant authorities with the view to receive further funding.