Adapted today, vulnerable tomorrow? Genomic landscapes of Italian goat breeds

Italian goat breeds represent a unique reservoir of livestock biodiversity shaped by environmental heterogeneity, historical trajectories, and long-standing management practices. Predominantly raised in extensive and semi-extensive systems, these populations are directly exposed to local conditions, favouring the development of adaptive traits while simultaneously increasing their sensitivity to ongoing climate change. We analysed genome-wide SNP data from 685 goats across 31 Italian populations, integrating temporal comparisons with samples collected approximately two decades ago (Italian Goat Consortium [1]) and a landscape genomics framework. This approach allowed us to jointly investigate how genomic diversity reflects geography and management, how it has changed over time, and how it relates to environmental adaptation and future vulnerability. Genomic diversity and structure closely mirrored geographic distribution, with clear differentiation between northern and central–southern populations, the latter displaying higher admixture levels. Temporal analyses showed overall stability of populations’ genomic composition but also revealed contrasting trajectories among breeds, including increased genetic homogenisation alongside rising inbreeding or, on the opposite side, shifts towards more admixed genomic backgrounds. These patterns highlight the impact of recent management and breeding practices on the genomic integrity of local populations. To investigate adaptation, we applied complementary genotype– environment association approaches (LFMM and pRDA), identifying hundreds of candidate loci associated with environmental gradients. The overlap between methods supported the robustness of the signals and the polygenic nature of adaptation and highlighted pathways potentially linked to adaptation and fitness, including immune response, oxidative stress, metabolism, and morphology. Future vulnerability was assessed through genomic offset under alternative climate scenarios. High offset values were heterogeneously distributed across Italy, and mainly concentrated along the northern Alpine fringe, the eastern Po Valley, and the Gargano area in Apulia. These findings support that some of the regions projected to undergo the most rapid environmental change correspond to areas where populations may be less genomically prepared to cope with these shifts, pointing to potential mismatches between current adaptive variation and future conditions [2]. Comparing past and present genomic patterns helps disentangle processes that maintain diversity from those that may erode it, while landscape genomics provides a forward- looking perspective on adaptive capacity. This integrated view provides a framework to distinguish resilient from potentially vulnerable populations and to guide conservation and breeding strategies aimed at preserving biodiversity while sustaining resilience under climate change [3]. Acknowledgements: Associazione Nazionale della Pastorizia (CHEESR and Sheep&Goat projects), in particular Alessio Negro and Silverio Grande; Next-GenerationEU (PNRR); Luigi Liotta and Mario Barbato (University of Messina). [1] Cortellari et al. The climatic and genetic heritage of Italian goat breeds with genomic SNP data. Scientific Reports, 11:10986, 2021 [2] Bionda et al. 70 years of heat waves and summer climate change affecting Italian small ruminant populations. Pastoralism, 14:12848, 2024 [3] Bionda et al. Spatio-temporal genomics of goats: recent evolution, adaptation, and future vulnerability. Animal, 20(1):101732, 2026