拥有150多个公认的品种,驴具有相关的经济重要性,尤其是在发展中国家。即使全世界的头估计数量为5300万,与其他牲畜物种相比,该物种受到的关注较少。意大利传统上被认为是欧洲驴繁殖的发源地之一,尽管生物多样性大量丧失,今天仍然有九个本土人口。使用双消化限制性位点相关DNA(ddRAD)测序对属于9个不同种群的220只动物进行了基因分型,以使用多技术方法研究多样性模式。总共产生了418,602,730个读段,并成功地解复用以获得具有约27K标记的中等密度SNP基因型组。多样性指数表现出中等水平的变异性。遗传距离和关系,与正在调查的驴种群的繁殖历史基本一致。结果强调了种群的分离是基于它们的遗传起源或繁殖区域之间的地理邻近性,显示低至中等水平的混合物,并表明在某些情况下存在明显的遗传差异。对于一些品种,结果也验证了适当的管理保护计划的成功。确定了ROH群岛,在与免疫反应和局部适应相关的基因组区域内映射,与以质朴和适应性闻名的物种的特征一致。这项研究是对意大利驴种群多样性的首次详尽的全基因组分析。结果强调了通过ddRAD方法检索的全基因组标记的高信息量。研究结果对设计和实施保护策略具有重要意义。驴物种的标准化基因型阵列将有可能合并全球数据集,以进一步了解基因组结构的进化和这一重要遗传资源的起源。
With more than 150 recognized breeds, donkeys assume relevant economic importance, especially in developing countries. Even if the estimated number of heads worldwide is 53M, this species received less attention than other livestock species. Italy has traditionally been considered one of the cradles of European
donkey breeding, and despite a considerable loss of biodiversity, today still counts nine autochthonous populations. A total of 220 animals belonging to nine different populations were genotyped using the double-digest restriction site associated DNA (ddRAD) sequencing to investigate the pattern of diversity using a multi-technique approach. A total of 418,602,730 reads were generated and successfully demultiplexed to obtain a medium-density SNP genotypes panel with about 27K markers. The diversity indices showed moderate levels of variability. The genetic distances and relationships, largely agree with the breeding history of the
donkey populations under investigation. The results highlighted the separation of populations based on their genetic origin or geographical proximity between breeding areas, showed low to moderate levels of admixture, and indicated a clear genetic difference in some cases. For some breeds, the results also validate the success of proper management conservation plans. Identified runs of homozygosity islands, mapped within genomic regions related to immune response and local adaptation, are consistent with the characteristics of the species known for its rusticity and adaptability. This study is the first exhaustive genome-wide analysis of the diversity of Italian
donkey populations. The results emphasized the high informativeness of genome-wide markers retrieved through the ddRAD approach. The findings take on great significance in designing and implementing conservation strategies. Standardized genotype arrays for
donkey species would make it possible to combine worldwide datasets to provide further insights into the evolution of the genomic structure and origin of this important genetic resource.
Donkeys assume relevant economic importance in several countries worldwide. However, the genetic structure of these populations is less investigated compared to other species. The aim of this study was to investigate the genetic background of nine different Italian
donkey populations. A total of 220 animals were genotyped with about 27K markers extracted by the double-digest restriction site associated DNA sequencing. The consistency of the results across different approaches agreed with the demographic history, the origin, and previous results on the nine donkey populations, suggesting that our conclusions are robust. Moreover, the results of the present study highlighted low to moderate levels of admixture and, for some breeds, confirmed the success of proper management conservation plans.