The mitogenome diversity of Alpine Rendena cattle: new clues on its maternal origin and the complex substructure of haplogroup T3

BACKGROUND: Val Rendena, an isolated Alpine valley in northern Italy, is home to an autochthonous, dual-purpose cattle breed with unique historical and morphological traits, which has been preserved by local breeders despite severe epidemics since the 1700s. While previous genome-wide studies identified signatures of selection in Rendena cattle, little is known about its evolutionary history. To address this issue, we analyzed complete mitogenomes from 137 Rendena individuals, selected to represent the majority of maternal lineages across the breed, as well as mitogenomes from 31 Alpine Grey individuals, purportedly closely related to Rendena cattle. RESULTS: We identified 86 distinct mitochondrial DNA (mtDNA) haplotypes in the Rendena breed, indicating a high haplotype diversity (Hd = 0.986). Phylogenetic analyses revealed that virtually all samples belong to the T macro-haplogroup (T3 = 91%; T2 = 7%; T5 = 1%), with only one falling within the Q1 lineage. The comparison with the 31 Alpine Grey mitogenomes (27 haplotypes; Hd = 0.989) revealed a strong genetic proximity of the two Alpine cattle populations, suggesting either a recent common ancestry or historical maternal gene flow. The presence of rare haplogroups (T5 and Q1) combined with a high overall mtDNA diversity suggests a complex history of the Rendena breed. Notably, the analysis of Rendena mtDNA variation within a West-Eurasian context revealed an ancestral link with the Balkans. However, no haplotype sharing was observed. This supports the uniqueness of the Rendena maternal gene pool. Finally, the high frequency of haplogroup T3 mitogenomes in our survey allowed us to re-assess and refine the global phylogeny of this haplogroup, revealing evidence of population structuring within the Rendena breed. CONCLUSIONS: Complete mitogenomes reveal that both Rendena and Alpine Grey cattle harbor high maternal diversity and preserve rare, ancient taurine lineages. The refined phylogeny of T3 demonstrates that this dominant European haplogroup is far more structured than previously recognized, reflecting complex post-domestication dispersal and regional differentiation. These findings underscore the value of local, endangered breeds as reservoirs of unique genetic variation and highlight the importance of their conservation for understanding cattle evolutionary history.