Exploring Genomic Variability in the Mediterranean Buffalo Breed: A Step Towards Custom SNP Array
Genomic improvement and sustainable breeding of Mediterranean buffalo are hampered by the lack of breed-specific genomic resources compared with bovine. To address this gap, we aimed to identify a comprehensive set of high-confidence single-nucleotide polymorphisms (SNPs) in Mediterranean buffalo and evaluate their informativeness across other buffalo populations. A total of 58 whole-genome sequencing samples, from three different sets, were merged through the integration of short- and long-read sequencing technologies. Variants, both unique and shared among datasets, were identified using a combination of bioinformatic tools to increase the reliability of the dataset. From these, over 11 million high-confidence biallelic SNPs were identified in the Mediterranean breed. The same SNPs were also tested in additional populations (other rivers and swamps) to evaluate their polymorphism and missingness. These results provide a robust genomic resource for Mediterranean buffalo, overcoming the limitations of bovine-derived genotyping tools available today. The identified SNPs dataset lays the basis for the development of a breed-specific SNP array, providing a dense and informative set of markers that could support cost-effective SNP chip development compared with existing arrays and sequencing technologies. This resource will facilitate more accurate genomic selection, precision breeding, and the conservation of genetic diversity in the Mediterranean buffalo population.
Authors
- Giovanni Vignali
- Elvira Toscano (ORCID: https://orcid.org/0000-0001-5013-5198)
- Arianna Manunza (ORCID: https://orcid.org/0000-0001-8812-8962)
- Daniele Pietrucci (ORCID: https://orcid.org/0000-0002-4233-0839)
- L. Iannuzzi (ORCID: https://orcid.org/0000-0002-5445-883X)
- Mayra Gómez Carpio (ORCID: https://orcid.org/0000-0002-3426-2231)
- Federica Di Maggio (ORCID: https://orcid.org/0009-0008-5917-1492)
- Marharyta Smal
- Salvatore Rubinacci
- Barbara Lazzari (ORCID: https://orcid.org/0000-0002-9558-914X)
- Francesco Salvatore (ORCID: https://orcid.org/0000-0002-2346-3564)
- Alessandro Rullo
- G. Cosenza (ORCID: https://orcid.org/0000-0001-6006-4987)
- Alessandro Weisz (ORCID: https://orcid.org/0000-0003-0455-2083)
- Federica Gabbianelli (ORCID: https://orcid.org/0000-0001-9010-0811)
- Paolo Cozzi (ORCID: https://orcid.org/0000-0003-0388-6874)
- Stefano Biffani (ORCID: https://orcid.org/0000-0001-5559-3630)
- Bianca Castiglioni (ORCID: https://orcid.org/0000-0003-2326-6701)
- Marcella Nunziato (ORCID: https://orcid.org/0000-0003-1999-4992)
- Francesca Rizzo (ORCID: https://orcid.org/0000-0003-1783-5015)
- Gabriele Di Vuolo (ORCID: https://orcid.org/0000-0001-9946-5999)
- Roberta Cimmino (ORCID: https://orcid.org/0000-0002-0146-1787)
- Ludovica Picarone
- Giovanni Chillemi
- Gabriella Porcai
- Leandra Sepe
- Francesca Bencivenga
- Marco Milanesi
- Chiara Arcuri
- Giovanni Paolella
Institutions
- Università Cattolica del Sacro Cuore (IT)
- University of Rome Tor Vergata (IT)
- University of Parma (IT)
- University of Salerno (IT)
- Università degli Studi della Tuscia (IT)
- Istituto per il Sistema Produzione Animale in Ambiente Mediterraneo (IT)
- Institute of Agricultural Biology and Biotechnology (IT)
- Federico II University Hospital (IT)
- ANT Foundation Italy Onlus (IT)
- CEINGE Biotecnologie Avanzate Franco Salvatore (Italy) (IT)
- Department of Agricultural Sciences (RU)
Publication Details
- Journal
- Animals
- Published
- 2026-03-15
- DOI
- https://doi.org/10.3390/ani16060922
- Primary Topic
- Genetic and phenotypic traits in livestock
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- Università degli Studi di Napoli Federico II
- European Commission