# Exploring Genomic Variability in the Mediterranean Buffalo Breed: A Step Towards Custom SNP Array

## TL;DR

This study identifies over 11 million SNPs in Mediterranean buffalo to support the development of a custom SNP array for breeding and conservation.

## Contribution

The study provides a high-confidence, breed-specific SNP dataset for Mediterranean buffalo, enabling more accurate genomic selection.

## Key findings

- Over 11 million high-confidence biallelic SNPs were identified in the Mediterranean buffalo breed.
- The SNPs are uniformly distributed across the genome, with one marker every 180 base pairs.
- The dataset supports the development of a cost-effective, breed-specific SNP array for buffalo.

## Abstract

Mediterranean buffalo is an important breed for the Italian livestock sector and agri-food system. However, genetic resources for this breed, and for buffalo in general, are limited compared with bovines. In this study, we analyzed the DNA of Mediterranean buffaloes to identify small differences in the genetic code, called single-nucleotide polymorphisms (SNPs), which can help distinguish individuals and associate them with phenotypes of interest for breeding. By combining different sequencing technologies and methodologies, we detected over eleven million high-quality variants in the Mediterranean breed. We also evaluated these variants in other buffalo populations (other rivers and swamps) to obtain a database for the buffalo species. Our results show that these markers cover the entire genome uniformly (with approximately 1 marker every 180 bp) and may reliably reflect buffalo genetic diversity. These results are instrumental in the development of buffalo genomic technologies, sustainable breeding, improving animal health and productivity, and contributing to the conservation of Mediterranean buffalo diversity.

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.