Genomic characterisation of local sheep breeds of the Eastern Alps

This study presents a comprehensive genomic characterisation and assessment of genetic erosion in four local sheep breeds from the Alpine Veneto region of Italy: Alpagota, Brogna, Foza and Lamon. Using a combination of principal component analysis, ADMIXTURE, and Fst distances, we identified genomic differentiation among the breeds, despite their shared ancestral origin—likely a result of long-term isolation between valleys. Notably, their genomic profiles exhibited greater affinity with Northern European breeds than with other Italian breeds, reflecting historical patterns of migration and trade. Analyses of effective population size (Ne), linkage disequilibrium (LD) and inbreeding levels revealed varying degrees of genetic diversity and erosion risk among the breeds. The Lamon and Foza populations showed critically low Ne, elevated LD and high inbreeding levels, indicating a heightened risk of genetic erosion—particularly for Foza. In contrast, Brogna and Alpagota maintained Ne estimates above 100, suggesting they are not currently at critical risk, though they still warrant proactive conservation measures to preserve genetic health. In conclusion, this study reveals distinct genomic patterns and differing conservation priorities among four Alpine Veneto sheep breeds. Genomic data proved essential in identifying breeds at critical risk—particularly Foza and Lamon—and in guiding tailored conservation strategies. Continued monitoring and proactive management are key to preserving their genetic integrity and long-term viability. The four Veneto breeds displayed genetic differences compared to other European breeds, likely as a result of long-term geographic isolation.Despite their relatedness, each breed remains genetically distinct.There is an urgent need for conservation actions, particularly for the highly vulnerable Foza population. The four Veneto breeds displayed genetic differences compared to other European breeds, likely as a result of long-term geographic isolation. Despite their relatedness, each breed remains genetically distinct. There is an urgent need for conservation actions, particularly for the highly vulnerable Foza population.

本研究针对意大利威尼托阿尔卑斯地区的四个地方绵羊品种——阿尔帕戈塔羊 (Alpagota)、布罗尼亚羊 (Brogna)、福扎羊 (Foza) 与拉蒙羊 (Lamon)，开展了全面的基因组特征分析与遗传侵蚀风险评估。本研究结合主成分分析 (principal component analysis, PCA)、ADMIXTURE软件分析与Fst遗传距离，明确了各品种间的基因组分化特征——尽管它们拥有共同的祖先起源，这一现象大概率源于山谷间长期的地理隔离。值得注意的是，相较于意大利其他绵羊品种，这四个品种的基因组特征与北欧绵羊品种更为相近，这反映了历史上的迁徙与贸易模式。通过对有效种群数量 (effective population size, Ne)、连锁不平衡 (linkage disequilibrium, LD) 以及近交水平的分析，研究揭示了各品种间存在不同程度的遗传多样性与遗传侵蚀风险。拉蒙羊与福扎羊的有效种群数量极低，连锁不平衡程度升高且近交水平较高，表明其遗传侵蚀风险显著升高，其中福扎羊的风险尤为严峻。相反，布罗尼亚羊与阿尔帕戈塔羊的有效种群数量估算值高于100，说明当前尚未处于临界风险状态，但仍需采取积极的保护措施以维持其遗传健康。综上，本研究揭示了威尼托阿尔卑斯地区四个绵羊品种各具独特的基因组模式与差异化的保护优先级。基因组数据对于甄别临界风险品种（尤其是福扎羊与拉蒙羊）、指导定制化保护策略至关重要。持续的监测与主动管理是维持其遗传完整性与长期生存能力的关键。相较于其他欧洲绵羊品种，这四个威尼托本地品种存在明显的遗传差异，这大概率源于长期的地理隔离。尽管彼此亲缘关系相近，每个品种仍保持了遗传独特性。当前亟需开展保护行动，针对高度濒危的福扎羊种群尤甚。相较于其他欧洲绵羊品种，这四个威尼托本地品种存在明显的遗传差异，这大概率源于长期的地理隔离。尽管彼此亲缘关系相近，每个品种仍保持了遗传独特性。当前亟需开展保护行动，针对高度濒危的福扎羊种群尤甚。