Conservation & local programs

Analysis of selection signatures reveals different adaptive strategies in five Italian beef cattle breeds

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Abstract

Marchigiana, Chianina, Romagnola, Maremmana, and Podolica are five autochthonous Italian cattle breeds specialized for beef production. Despite common Podolian origins, they have adapted to diverse harsh and low input environments across Central and Southern Italy. Among them, Maremmana and Podolica are more rustic and adapted to extensive systems and extreme climatic conditions, while the other breeds are more specialized for beef productions. The genomics of these breeds have only recently begun to be investigated, and knowledge on their evolution and selection history still relies on historical records and herd books, which were established in the early 20th century. Nonetheless, these breeds have an ancient documentation history, with evidence of their presence in Italy for over 22 centuries. This work aimed to explore the adaptive signals by investigating the selection signatures in the breeds. For each breed, two groups were considered: animals from the population and young bulls undergoing a performance test at the ANABIC genetic station, representing approximately 26% of the total. Therefore, the analysis considered a total of 4,639 Marchigiana, 4,817 Chianina, 2,296 Romagnola, 1,057 Maremmana, and 2,898 Podolica genotyped animals. All the animals were genotyped using a 33K SNP chip array. iHS and XP-EHH analysis were performed within both breed and group separately, with rehh R package. Regarding XP-EHH analysis, each breed was tested against a reference population composed of the remaining four breeds. Significant 100kb windows were considered as candidate regions and kept for further analysis irrespective of whether they were detected on both groups and/or supported by both iHS and XP-EHH analysis. Genes located in such regions were retrieved via BioMart, and QTLs were annotated and enriched via GALLO R package. Results indicated several candidate regions shared across the breeds. QTL annotations highlighted reproduction-related loci specific to Romagnola compared with the other breeds. Marchigiana and Maremmana exhibited a clear different adaptive background compared to Romagnola and Chianina, with the resulting QTLs dominated by production and meat & carcass related QTLs, driven by a significant region on BTA6, harboring several genes associated with growth and muscularity (i.e., LCORL, SLIT). Finally, the uttermost rusticity of Podolica was evidenced by an almost even distribution of QTLs classes under selection. Several QTLs commonly associated to milk traits were found, suggesting that conserved genes may have a pleiotropic effect on traits of different aptitudes. These findings confirm the different evolution and selection history of the five Italian beef cattle breeds and provide novel insights into their genomic adaptation to different environments. Finally, deepened knowledge on local breeds genomics is essential for developing effective breeding strategies and to valorize these valuable local genetic resources.

Keywords: 2026

How to Cite:

Colombi, D., Gomez Proto, G., Perini, F., Mancin, E., Sbarra, F., Quaglia, A., Tiezzi, F., Mantovani, R., Lasagna, E. & Sartori, C., (2026) “Analysis of selection signatures reveals different adaptive strategies in five Italian beef cattle breeds”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286294. doi: https://doi.org/10.31274/wcgalp.23910

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