Conservation & local programs

High-Resolution Genomic Assessment of Diversity and Conservation Risks in Croatian Indigenous Cattle

---

Abstract

The domestication and subsequent migrations of cattle profoundly shaped the genetic landscape of European bovine populations, with the Balkan Peninsula serving as a major corridor for livestock dispersal. Croatian indigenous cattle - Buša (CCB), Istrian (CCIG), and Slavonian-Syrmian Podolian (CCSSP) - represent locally adapted breeds of cultural and agricultural significance, yet all three are threatened due to small census sizes and/or potential crossbreeding. This study assessed their conservation status by evaluating genomic diversity, inbreeding (FROH), effective population size (Ne), population structure, admixture, and relatedness to 22 globally distributed breeds using high-density genomic data (Illumina BovineHD, 777K SNPs). A total of 674 individuals were analyzed, including 112 newly genotyped animals from the three Croatian breeds (CCB: n=40; CCIG: n=40; CCSSP: n=32), while data for other breeds were sourced from public repositories. Contemporary Ne estimates obtained with GONE indicated small Ne in all Croatian breeds (CCB = 138; CCIG = 60; CCSSP = 43), reflecting strong demographic contraction in recent generations. Historical Ne estimates (30 generations back) revealed drastic reductions by factors of 138 (CCB), 100 (CCIG), and 8 (CCSSP), highlighting long-term genetic erosion. ROH-based inbreeding coefficients were high in CCIG (FROH >1Mb= 0.23; FROH >8Mb=0.07) and CCSSP (FROH >1Mb=0.23; FROH >8Mb=0.09), exceeding those observed in Holstein cattle. In contrast, CCB exhibited considerably lower remote inbreeding (FROH >1Mb=0.13; FROH >8Mb=0.05). For all three breeds, FIS did not differ significantly from zero, suggesting that avoidance of close-relative matings has been practiced. Contrary to expectations based on phenotype, CCB and CCIG showed low pairwise differentiation (FST=0.05), while both CCB versus CCSSP and CCIG versus CCSSP were more strongly differentiated (FST=0.10). Neighbor-net analysis grouped CCSSP with Maltese and Romanian Grey cattle, consistent with their Podolian background, although the absence of Hungarian Grey and Serbian Podolian data limits phylogenetic resolution. POPVAE dimensionality reduction clearly separated all Croatian breeds, while ADMIXTURE revealed strong genetic distinctiveness of CCIG and CCSSP and pronounced admixture in CCB. Migration analyses did not detect recent gene flow among the Croatian breeds or between them and neighboring local populations. Overall, these findings demonstrate that CCB, CCIG, and CCSSP are genetically vulnerable and require strengthened diversity-oriented breeding strategies. CCIG and CCSSP are particularly at risk due to high inbreeding and very small population sizes, suggesting potential accumulation of genetic load. Although CCB maintains a larger Ne and lower historical inbreeding, its substantial admixture indicates insufficient breed homogenization and underscores the need for improved management to preserve its genetic identity.

Keywords: 2026

How to Cite:

Mijadzikovic, Z., Cubric-Curik, V., Ferenčakovič, M., Vostrý, L. & Curik, I., (2026) “High-Resolution Genomic Assessment of Diversity and Conservation Risks in Croatian Indigenous Cattle”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286995. doi: https://doi.org/10.31274/wcgalp.24190

Rights: 1