Czech J. Anim. Sci., X:X | DOI: 10.17221/138/2025-CJAS

Population structure, genetic diversity, and reproductive efficiency in the autochthonous Busha cattle breedOriginal Paper

Aneta Piplica ORCID...1, Mato Čačić ORCID...2, Anamaria Ekert Kabalin ORCID...1, Maja Maurić Maljković ORCID...1, Ivan Vlahek ORCID...1, Velimir Sušić ORCID...1, Sven Menčik ORCID...1
1 Department of Animal Breeding and Livestock Production, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
2 Directorate for Livestock and Food Quality, Ministry of Agriculture, Forestry and Fisheries, Zagreb, Croatia

Autochthonous cattle breeds represent important resources of genetic diversity. The Busha cattle breed is reared in the Balkan Peninsula and is characterised by high adaptability, resilience, longevity, small body size, and low maintenance and production requirements. During the 36-year observation period, the total population of the autochthonous Busha cattle breed in the Republic of Croatia amounted to 10 411 animals. Pedigree completeness for the total population, considering the first parental generation, was 97.1%. The average inbreeding coefficient was 2.44%, ranging from zero to 42.6%, while the average relatedness coefficient was 3.56% in the total population. The effective population size, calculated in the reference population based on the individual increase in inbreeding, was 63.3. The probabilities of gene origin in the reference population were fe – 38.0, fa – 33.0, and fg – 25.4, indicating a loss of genetic variability due to genetic drift (fg/fe – 0.66) and a bottleneck (fe/fa – 1.15). In the population of the autochthonous Busha cattle breed, the effective number of ancestors (fa) was smaller than the effective number of founders (fe). Increased relatedness among animals was observed, which could affect the long-term conservation of the population.

Keywords: conservation; bovine; fertility traits; genetic variation; inbreeding; pedigree analysis

Received: October 9, 2025; Accepted: December 16, 2025; Prepublished online: January 26, 2026 

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    References

    1. Ablondi M, Sabbioni A, Stocco G, Cipolat-Gotet C, Dadousis C, van Kaam JT, Finocchiaro R, Summer A. Genetic diversity in the Italian Holstein dairy cattle based on pedigree and SNP data prior and after genomic selection. Front Vet Sci. 2022 Jan 13;8:773985. Go to original source... Go to PubMed...
    2. Ballou JD, Lacy RC. Identifying genetically important individuals for management of genetic variation in pedigreed populations. In: Ballou JD, Gilpin M, Foose TJ, editors. Population management for survival and recovery: Analytical methods and strategies in small population conservation. New York (NY): Columbia University Press; 1995. p. 76-111.
    3. Biscarini F, Mastrangelo S, Catillo G, Senczuk G, Ciampolini R. Insights into genetic diversity, runs of homozygosity and heterozygosity-rich regions in Maremmana semi-feral cattle using pedigree and genomic data. Animals (Basel). 2020 Dec 3;10(12):2285. Go to original source... Go to PubMed...
    4. Boichard D, Maignel L, Verrier E. The value of using probabilities of gene origin to measure genetic variability in a population. Genet Sel Evol. 1997;29(1):5-23. Go to original source...
    5. Bosse M, van Loon S. Challenges in quantifying genome erosion for conservation. Front Genet. 2022 Sep 26;13:960958. Go to original source... Go to PubMed...
    6. Bunevski G, Nikitovic J, Saltamarski Z. Conservation of the genetic material of Macedonian Busha cattle. Acta Agric Serb. 2016;21(41):17-24. Go to original source...
    7. Canas-Alvarez JJ, Gonzalez-Rodriguez A, Martin-Collado D, Aviles C, Altarriba J, Baro JA, de la Fuente LF, Diaz C, Molina A, Varona L, Piedrafita J. Monitoring changes in the demographic and genealogical structure of the main Spanish local beef breeds. J Anim Sci. 2014 Oct;92(10):4364-74. Go to original source... Go to PubMed...
    8. Carolino N, Vitorino A, Carolino I, Pais J, Henriques N, Silveira M, Vicente A. Genetic diversity in the Portuguese Mertolenga cattle breed assessed by pedigree analysis. Animals (Basel). 2020 Oct 29;10(11):1990. Go to original source... Go to PubMed...
    9. Cortes O, Sevane N, Baro JA, Canon J. Pedigree analysis of a highly fragmented population, the Lidia cattle breed. Livest Sci. 2014 Jul;167:1-8. Go to original source...
    10. Curone G, Filipe J, Cremonesi P, Trevisi E, Amadori M, Pollera C, Castiglioni B, Turin L, Tedde V, Vigo D, Moroni P, Minuti A, Bronzo V, Addis MF, Riva F. What we have lost: Mastitis resistance in Holstein Friesians and in a local cattle breed. Res Vet Sci. 2018 Feb;116 (Suppl):88-98. Go to original source... Go to PubMed...
    11. Fabbri MC, Goncalves de Rezende MP, Dadousis C, Biffani S, Negrini R, Souza Carneiro PL, Bozzi R. Population structure and genetic diversity of Italian beef breeds as a tool for planning conservation and selection strategies. Animals (Basel). 2019 Nov 1;9(11):880. Go to original source... Go to PubMed...
    12. Felius M, Beerling ML, Buchanan DS, Theunissen B, Koolmees PA, Lenstra JA. On the history of cattle genetic resources. Diversity (Basel). 2014 Nov 12;6(4):705-50. Go to original source...
    13. Garcia-Atance MA, Carleos C, Andrino S, Justo JR, Rivero CJ, Fernandez M, Canon J, Cortes O. Genetic diversity of five Galician (Northwestern Spain) local primitive bovine breeds using pedigree records. Diversity (Basel). 2023 Feb 10;15(2):252. Go to original source...
    14. Gutierrez JP, Goyache F. A note on ENDOG: A computer program for analysing pedigree information. J Anim Breed Genet. 2005 Jun;122(3):172-6. Go to original source... Go to PubMed...
    15. Howard JT, Pryce JE, Baes C, Maltecca C. Invited review: Inbreeding in the genomics era: Inbreeding, inbreeding depression, and management of genomic variability. J Dairy Sci. 2017 Aug;100(8):6009-24. Go to original source... Go to PubMed...
    16. Hristov P, Sirakova D, Mitkov I, Spassov N, Radoslavov G. Balkan brachicerous cattle - The first domesticated cattle in Europe. Mitochondrial DNA A DNA Mapp Seq Anal. 2018 Jan;29(1):56-61. Go to original source... Go to PubMed...
    17. Hunter ME, Hoban SM, Bruford MW, Segelbacher G, Bernatchez L. Next-generation conservation genetics and biodiversity monitoring. Evol Appl. 2018 Aug;11(7):1029-34. Go to original source... Go to PubMed...
    18. Ivankovic A, Ramljak J, Subara G, Pecina M, Suran E, Ivkic Z, Konjacic M. Evaluation of the Istrian cattle population structure by pedigree analysis. In: Proceedings of the 12th World Congress on Genetics Applied to Livestock Production (WCGALP); 2022 Jul 3-8; Rotterdam (Netherlands). Wageningen (Netherlands): Wageningen Academic Publishers; 2022. p. 919-22. Go to original source...
    19. James JW. A note on selection differentials and generation length when generations overlap. Anim Prod. 1977 Feb;24(1):109-12. Go to original source...
    20. Jarnecka O, Bauer EA, Jagusiak W. Pedigree analysis in the Polish Red cattle population. Animal. 2021 Jun;15(6):100238. Go to original source... Go to PubMed...
    21. Lacy RC. Analysis of founder representations in pedigrees: Founder equivalents and founder genome equivalents. Zoo Biol. 1989;8(2):111-23. Go to original source...
    22. Leroy G, Baumung R, Boettcher P, Besbes B, From T, Hoffmann I. Animal genetic resources diversity and ecosystem services. Glob Food Secur. 2018 Jun;17:84-91. Go to original source...
    23. MacCluer JW, Boyce AJ, Dyke B, Weitkamp LR, Pfenning DW, Parsons CJ. Inbreeding and pedigree structure in Standardbred horses. J Hered. 1983 Nov-Dec;74(6):394-9. Go to original source...
    24. Maignel L, Boichard D, Verrier E. Genetic variability of French dairy breeds estimated from pedigree infor-mation. Interbull Bull. 1996;14:49-54.
    25. Meuwissen TI, Luo Z. Computing inbreeding coefficients in large populations. Genet Sel Evol. 1992;24(4):305-13. Go to original source...
    26. Nyman S, Johansson AM, Palucci V, Schonherz AA, Guldbrandtsen B, Hinrichs D, de Koning DJ. Inbreeding and pedigree analysis of the European red dairy cattle. Genet Sel Evol. 2022 Oct 23;54(1):70. Go to original source... Go to PubMed...
    27. Papachristou D, Koutsouli P, Laliotis GP, Kunz E, Upadhyay M, Seichter D, Russ I, Gjoko B, Kostaras N, Bizelis I, Medugorac I. Genomic diversity and population structure of the indigenous Greek and Cypriot cattle populations. Genet Sel Evol. 2020 Jul 29;52(1):43. Go to original source... Go to PubMed...
    28. Ramljak J, Bunevski G, Bytyqi H, Markovic B, Brka M, Ivankovic A, Kume K, Stojanovic S, Nikolov V, Simcic M, Solkner J, Kunz E, Rothammer S, Seichter D, Grunenfelder HP, Broxham ET, Kugler W, Medugorac I. Conservation of a domestic metapopulation structured into related and partly admixed strains. Mol Ecol. 2018 Apr;27(7):1633-50. Go to original source... Go to PubMed...
    29. Santana ML, Pereira RJ, Bignardi AB, Ayres DR, Menezes GRO, Silva LOC, Leroy G, Machado CHC, Josahkian LA, Albuquerque LG. Structure and genetic diversity of Brazilian Zebu cattle breeds assessed by pedigree analysis. Livest Sci. 2016 May;187:6-15. Go to original source...
    30. Schiavo G, Bovo S, Ribani A, Moscatelli G, Bonacini M, Prandi M, Mancin E, Mantovani R, Dall'Olio S, Fontanesi L. Comparative analysis of inbreeding parameters and runs of homozygosity islands in 2 Italian autochthonous cattle breeds mainly raised in the Parmigiano-Reggiano cheese production region. J Dairy Sci. 2022 Mar;105(3):2408-25. Go to original source... Go to PubMed...
    31. Shaw RE, Farquharson KA, Bruford MW, Coates DJ, Elliott CP, Mergeay J, Ottewell KM, Segelbacher G, Hvilsom C, Perez-Espona S, Rungis D, Aravanopoulos F, Bertola LD, Cotrim H, Cox K, Cubric-Curik V, Ekblom R, Godoy JA, Konopinski MK, Laikre L, Russo IM, Velickovic N, Vergeer P, Vila C, Brajkovic V, Field DL, Goodall-Copestake WP, Hailer F, Hopley T, Zachos FE, Alves PC, Biedrzycka A, Binks RM, Buiteveld J, Buzan E, Byrne M, Huntley B, Iacolina L, Keehnen NLP, Klinga P, Kopatz A, Kurland S, Leonard JA, Manfrin C, Marchesini A, Millar MA, Orozco-terWengel P, Ottenburghs J, Posledovich D, Spencer PB, Tourvas N, Unuk Nahberger T, van Hooft P, Verbylaite R, Vernesi C, Grueber CE. Global meta-analysis shows action is needed to halt genetic diversity loss. Nature. 2025 Feb;638(8051):704-10. Go to original source... Go to PubMed...
    32. Star B, Spencer HG. Effects of genetic drift and gene flow on the selective maintenance of genetic variation. Genetics. 2013 May;194(1):235-44. Go to original source... Go to PubMed...
    33. Villanueva B, Fernandez A, Saura M, Caballero A, Fernandez J, Morales-Gonzalez E, Toro MA, Pong-Wong R. The value of genomic relationship matrices to estimate levels of inbreeding. Genet Sel Evol. 2021 May 1;53(1):42. Go to original source... Go to PubMed...
    34. Wang J, Santiago E, Caballero A. Prediction and estimation of effective population size. Heredity (Edinb). 2016 Oct;117(4):193-206. Go to original source... Go to PubMed...
    35. Wellmann R, Bennewitz J. Key genetic parameters for population management. Front Genet. 2019 Aug 16;10:667. Go to original source... Go to PubMed...

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