Genetic diversity, gene flow, and sire networks in the Italian Mediterranean buffalo: insights from SNP-based genomic data

The Italian Mediterranean Buffalo is an economically and culturally important breed whose long-term sustainability depends on effective genetic management. In this study, the genetic diversity and population structure of the IMB were investigated across 10 Italian geographic areas using data from 4,505 animals genotyped with the Axiom Buffalo Genotyping Array 90K. By integrating high-density genomic analyses with sire network modelling, this study provides a novel framework to simultaneously characterise the genetic state of the population and the reproductive mechanisms driving it. Mean observed and expected heterozygosity values were 0.384 and 0.380, respectively. The mean inbreeding coefficient was positive in six areas, mainly in central and northern Italy. Average genetic differentiation between areas was 1.53%, while principal component analysis confirmed a distinct cluster of individuals from the Caserta area. Analysis of sire gene flow revealed that genetic diversity is unevenly distributed. Core groups, Caserta, Salerno, and Latina, act as central hubs in the sire flow network, concentrating most reproductive output, while peripheral groups depend on few sire source. The effectiveness of gene flow depends not only on the number of incoming sires but also on their genetic complementarity with the recipient group, as importing many genetically similar sires contributes little to allelic renewal. Integrating sire gene flow and network dynamics into breeding programs can guide efforts to broaden sire contribution, prioritise genetically distinct sources, and reduce reproductive monopolies. Combined with continuous genomic monitoring, these measures should help preserve allelic richness and ensure the long-term sustainability, adaptability, and productivity of the breed.