Sequencing & Pangenomes

Uncovering Copy Number Variation in Native Alpine Cattle Breeds Using a Multi-Caller Consensus Approach

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Abstract

Copy number variants (CNVs), structural variations larger than 1 kb, represent a major source of genomic diversity and may influence adaptive and production traits. Autochthonous and locally adapted Alpine cattle breeds are valuable reservoirs of diversity, yet CNVs remain under-characterized in these populations. This study aimed to characterize CNVs in Alpine cattle using whole-genome sequencing and a multi-caller consensus approach. We analysed whole-genome sequencing data from 101 individuals representing eight Alpine cattle breeds: Aosta Black Pied (ABP), Aosta Chestnut-Hérens (ACH), Aosta Red Pied (ARP), Fleckvieh (FLK), Original Brown Swiss (OBS), Pinzgauer (PNZ), Rätisches Grauvieh (RGV), and Tiroler Grauvieh (TGV). Reads were aligned to the ARS-UCD1.2 reference genome using BWA-MEM2 within the nf-core Sarek pipeline. CNVs were detected using three complementary tools, and raw variant calls were filtered to retain high-confidence deletions and duplications between 1 kb and 5 Mb. Tool-specific quality criteria were applied: CNVnator (p 0), Manta (FILTER=PASS), and Delly (FILTER=PASS; ≥3 supporting reads including PE/DV/SR). These filtered CNVs were merged within individuals to define consensus CNVs that were merged across individuals using bedtools (≥90% reciprocal overlap) to define high-confidence CNV regions (CNVRs). Additional filters excluded CNVs located on unplaced contigs. Gene content within CNVRs was annotated using the HandyCNV R package. The multi-caller CNV discovery approach identified 59,548, 311,585 and 295,404 raw CNVs using CNVnator, Delly and Manta, respectively. After quality filtering and cross-tool integration, the per-individual consensus dataset comprised 236,547 high-confidence CNVs, with deletions markedly outnumbering duplications (208,016 DEL vs 28,531 DUP). Collapsing individual CNVs resulted in 22,909 intra-breed CNVRs (18,088 DEL; 4,500 DUP; 321 MIX) and 4,325 inter-breed CNVRs (3,578 DEL; 747 DUP), supporting a shared structural variation landscape across Alpine breeds. Focusing on highly conserved variation, we identified 101 core inter-breed CNVRs present in all eight breeds, distributed across multiple autosomes. Functional annotation revealed 12 gene-overlapping core CNVRs, including loci harbouring genes previously associated with environmental adaptation and stress resilience in bovines, such as PIK3C2G (altitude-related CNVR differentiation, CNVR_6) and UQCR10 (oxidative phosphorylation and hypoxia-related pathways, CNVR_69), as well as PDE5A and CASTOR1 (heat-stress response, CNVR_13 and CNVR_69) and MACROD2 (fitness-related traits, CNVR_44). The identification of a limited set of core CNVRs shared by all breeds, provides a valuable resource to investigate structural variation potentially contributing to resilience in mountainous environments. Research supported by the DUALBREEDING project - PSRN 2014/2020 and funded by the European Union - Next Generation EU, Mission 4 Component 1, CUP G53D23004040006 - PRIN 2022 "GENOmic Breeding VALue Estimation in a Native Alpine Cattle Breed."

Keywords: 2026

How to Cite:

Bernini, F., Sioli, L., Gomez Proto, G., Ferrari, C., Mancin, E., Sartori, C., Mantovani, R., Bagnato, A. & Strillacci, M., (2026) “Uncovering Copy Number Variation in Native Alpine Cattle Breeds Using a Multi-Caller Consensus Approach”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2285620. doi: https://doi.org/10.31274/wcgalp.23756

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