Assessment of Heterozygosity in European Local and Cosmopolitan Pig Populations

Maria Chiara Fabbri (), Katherine D. Arias, Marcos P. G. Rezende, Francesco Tiezzi, Stefano Biffani, Felix Goyache, Giuseppina Schiavo, Samuele Bovo, Luca Fontanesi, Marjeta Čandek-Potokar, Maria Muñoz, Cristina Ovilo, Klavdija Poklukar, Martin Škrlep and Riccardo Bozzi
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Maria Chiara Fabbri: Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università di Firenze, 50144 Firenze, Italy
Katherine D. Arias: Área de Genética y Reproducción Animal, SERIDA-Deva, 33394 Gijón, Spain
Marcos P. G. Rezende: Associazione Nazionale Allevatori Razza Bruna, Bussolengo, 37012 Verona, Italy
Francesco Tiezzi: Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università di Firenze, 50144 Firenze, Italy
Stefano Biffani: Institute of Agricultural Biology and Biotechnology-CNR, 20133 Milano, Italy
Felix Goyache: Área de Genética y Reproducción Animal, SERIDA-Deva, 33394 Gijón, Spain
Giuseppina Schiavo: Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, 40127 Bologna, Italy
Samuele Bovo: Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, 40127 Bologna, Italy
Luca Fontanesi: Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, 40127 Bologna, Italy
Marjeta Čandek-Potokar: Kmetijski Inštitut Slovenije, Hacquetova ulica 17, 1000 Ljubljana, Slovenia
Maria Muñoz: Departamento Mejora Genética Animal, INIA-CSIC, Crta. de la Coruña, km. 7,5, 28040 Madrid, Spain
Cristina Ovilo: Departamento Mejora Genética Animal, INIA-CSIC, Crta. de la Coruña, km. 7,5, 28040 Madrid, Spain
Klavdija Poklukar: Kmetijski Inštitut Slovenije, Hacquetova ulica 17, 1000 Ljubljana, Slovenia
Martin Škrlep: Kmetijski Inštitut Slovenije, Hacquetova ulica 17, 1000 Ljubljana, Slovenia
Riccardo Bozzi: Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università di Firenze, 50144 Firenze, Italy

Agriculture, 2025, vol. 15, issue 7, 1-14

Abstract: Researchers focused on assessing differences in gene diversity within and between populations, whether cosmopolitan or local. However, the identification of patterns of variation in non-random heterozygous genomic stretches, known as Heterozygosity-Rich regions (HRRs), has not yet been determined in European local pig breeds. A total of 23 pig breeds (20 local and 3 cosmopolitan) were assessed and compared in terms of heterozygosity-rich regions. The breeds with the highest number of HRRs were Large White, Lithuanian Old type, and Landrace, followed by Lithuanian Native, Mora Romagnola, and Duroc. The breeds with the lowest number were Alentejana, Iberian, and Majorcan Black. No shared HRR islands were found in all breeds, but gene enrichment analysis performed in the most common HRRs revealed several biologically important genes that cluster together and play significant roles, primarily related to the immune system. Permutation analysis indicated that some local breeds serve as true reservoirs of genetic diversity, displaying distinct and unique characteristics in terms of heterozygosity. This study suggests the importance of investigating heterozygosity to develop a comprehensive picture of pig breeds, regardless of the production system, country of origin, or population size.

Keywords: autochthonous breed; fitness; heterozygosity-rich regions; runs of heterozygosity; Sus scrofa (search for similar items in EconPapers)
JEL-codes: Q1 Q10 Q11 Q12 Q13 Q14 Q15 Q16 Q17 Q18 (search for similar items in EconPapers)
Date: 2025
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