Placing Varzese-Ottonese-Tortonese dual-purpose cattle breed in the genetic landscape of cattle genetic resources

The Varzese, also known as Ottonese or Tortonese, is an indigenous cattle breed originated in Lombardy and is primarily raised in the mountainous regions of the Appennino Lombardo. Over time, its population has significantly declined due to competition from agricultural mechanization and the dominance of higher-yielding cosmopolitan breeds. By the 1990s, the breed had reached critically low numbers. However, biodiversity conservation efforts and the recognition of its high-quality meat and milk products have contributed to its revival. This study aimed to analyse the population structure and identify selection signatures in the Varzese breed (n = 82), comparing it with two closely related Italian autochthonous cattle breeds: Reggiana (n = 196) and Modenese (n = 92). Using high-density single-nucleotide polymorphism (SNP) chip data, we performed population structure analyses, including multidimensional scaling, genetic admixture analysis, and linkage disequilibrium decay. Selection signatures were detected using multiple approaches, such as runs of homozygosity (ROH), fixation index (FST), integrated haplotype score (iHS), and cross-population extended haplotype homozygosity (XP-EHH). Our results indicate a strong genetic relationship between the Varzese and Reggiana breeds, with notable selection sweeps along the Varzese genome. The annotation of these selected regions revealed genes linked to key traits relevant to dairy and beef production, underscoring potential avenues for genetic improvement and conservation. This study provides a comprehensive genomic characterisation that can guide future breeding and conservation strategies for this endangered cattle breed. This research was funded by the PSRN (Programma di Sviluppo Rurale Nazionale) 2014–2020 and 2020–2023, measure 10.2, Dual Breeding and Dual Breeding 2 projects.