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Genetic Diversity and Candidate Selection Signatures in Hungarian and Romanian Carpathian Water Buffalo Inferred from Cross-Species SNP-Array Genotyping
by
, , , , and
Szilvia Kusza
1,*, 
Putri Kusuma Astuti
1,
Daniela Elena Ilie
2,
Szilárd Pinnyey
3,
Bettina Hegedűs
1,
Husein Ohran
4,
Zoltán Bagi
1 and
Dinu Gavojdian
5 1
Centre for Agricultural Genomics and Biotechnology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
2
Research and Development Station for Bovine, Bodrogului 32, 310059 Arad, Romania
3
Institute of Animal Sciences and Wildlife Management, University of Szeged, 6800 Hódmezővásárhely, Hungary
4
Department of Physiology, University of Sarajevo, Zmaja od Bosne 90, 71000 Sarajevo, Bosnia and Herzegovina
5
Research and Development Institute for Bovine, Balotesti, Bucuresti-Ploiesti km 21, 077015 Ilfov, Romania
*
Author to whom correspondence should be addressed.
Animals 2026, 16(14), 2120; https://doi.org/10.3390/ani16142120
Submission received: 8 June 2026
/
Revised: 26 June 2026
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Accepted: 3 July 2026
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Published: 8 July 2026
(This article belongs to the Special Issue Livestock and Poultry Genetics and Breeding Management)
Simple Summary
The Carpathian water buffalo is a regional livestock resource in Central and Eastern Europe, but little is known about its genetic background. This study compared buffalo from Hungary and Romania using genome-wide marker data generated with a cattle genotyping array. The results show that both populations retain moderate genetic diversity. The Romanian animals had slightly higher diversity, whereas the Hungarian animals showed more long homozygous genome segments, which may indicate stronger recent relatedness or a more restricted breeding structure. The candidate regions for positive selection included genomic regions that may be associated with immune response, reproduction, growth, milk production and heat or cold tolerance. Because the marker array was designed for cattle and sample sizes differed between countries, the findings should be considered a first genomic baseline rather than final evidence of causal variants. The results can support future conservation planning and more detailed studies using buffalo-specific genomic tools.
Abstract
The Carpathian water buffalo represents a locally adapted but under-characterized genetic group found in Central and Eastern Europe. Genome-wide information on its genetic diversity, population structure and potential adaptive variation remains limited, particularly for Hungarian and Romanian populations. In this study, we genotyped 263 water buffalo individuals from Hungary and Romania using the GeneSeek Genomic Profiler Bovine 100K SNP array to evaluate genetic diversity, the population structure, runs of homozygosity (ROH) and candidate genomic regions showing signatures of selection. After quality control, 214 Hungarian and 33 Romanian individuals and 6605 SNPs were retained for downstream analyses. Both populations showed moderate genetic diversity, with the Romanian population displaying higher minor allele frequency, observed heterozygosity and nucleotide diversity than the Hungarian population. In contrast, the Hungarian buffalo showed a higher burden of runs of homozygosity, including a larger proportion of long ROH segments, suggesting stronger recent autozygosity or a more restricted breeding structure. Principal component analysis and neighbor-joining phylogeny separated the two populations, whereas ADMIXTURE indicated shared ancestry and a within-population substructure rather than complete population-specific differentiation. The integration of standardized FST, absolute allele-frequency differences and ROH islands identified six candidate regions under a positive signature of selection in each population. These regions harbored genes previously associated with immune response, reproduction, growth, milk production and thermotolerance in bovids. Functional enrichment was limited, with significant Gene Ontology terms detected only in the Hungarian candidate regions. Our results provide a regional genomic baseline for the future conservation and breeding management of Carpathian water buffalo. Given the use of a cross-species SNP array and unequal sample sizes, the candidate selection signals should be interpreted as hypothesis-generating and warrant validation using higher-density buffalo-specific genomic data.
