Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, 90128, Palermo, Italy.
Dipartimento di Bioscienze Biotecnologie e Biofarmaceutica, University of Bari, 70124, Bari, Italy.
Genet Sel Evol. 2018 Jun 26;50(1):35. doi: 10.1186/s12711-018-0406-x.
In the last 50 years, the diversity of cattle breeds has experienced a severe contraction. However, in spite of the growing diffusion of cosmopolite specialized breeds, several local cattle breeds are still farmed in Italy. Genetic characterization of breeds represents an essential step to guide decisions in the management of farm animal genetic resources. The aim of this work was to provide a high-resolution representation of the genome-wide diversity and population structure of Italian local cattle breeds using a medium-density single nucleotide polymorphism (SNP) array.
After quality control filtering, the dataset included 31,013 SNPs for 800 samples from 32 breeds. Our results on the genetic diversity of these breeds agree largely with their recorded history. We observed a low level of genetic diversity, which together with the small size of the effective populations, confirmed that several breeds are threatened with extinction. According to the analysis of runs of homozygosity, evidence of recent inbreeding was strong in some local breeds, such as Garfagnina, Mucca Pisana and Pontremolese. Patterns of genetic differentiation, shared ancestry, admixture events, and the phylogenetic tree, all suggest the presence of gene flow, in particular among breeds that originate from the same geographical area, such as the Sicilian breeds. In spite of the complex admixture events that most Italian cattle breeds have experienced, they have preserved distinctive characteristics and can be clearly discriminated, which is probably due to differences in genetic origin, environment, genetic isolation and inbreeding.
This study is the first exhaustive genome-wide analysis of the diversity of Italian cattle breeds. The results are of significant importance because they will help design and implement conservation strategies. Indeed, efforts to maintain genetic diversity in these breeds are needed. Improvement of systems to record and monitor inbreeding in these breeds may contribute to their in situ conservation and, in view of this, the availability of genomic data is a fundamental resource.
在过去的 50 年中，牛种的多样性经历了严重的收缩。然而，尽管越来越多的世界性专门品种扩散，意大利仍有几个本地牛种在养殖。品种的遗传特征是指导农场动物遗传资源管理决策的重要步骤。本研究旨在使用中密度单核苷酸多态性（SNP）阵列提供意大利本地牛种全基因组多样性和群体结构的高分辨率描述。
经过质量控制过滤后，该数据集包括 31013 个 SNP，用于来自 32 个品种的 800 个样本。我们对这些品种遗传多样性的研究结果与它们的记录历史基本一致。我们观察到遗传多样性水平较低，加上有效种群规模较小，证实了一些品种受到灭绝的威胁。根据纯合子运行分析，一些本地品种，如加法尼亚纳、穆卡皮萨纳和蓬特雷莫莱，存在近期近交的强烈证据。遗传分化、共同祖先、混合事件和系统发育树的模式都表明存在基因流，特别是在起源于同一地理区域的品种之间，如西西里品种。尽管大多数意大利牛种经历了复杂的混合事件，但它们保留了独特的特征，可以清楚地区分，这可能是由于遗传起源、环境、遗传隔离和近亲繁殖的差异所致。
本研究是对意大利牛种多样性进行的首次全面全基因组分析。研究结果具有重要意义，因为它们有助于设计和实施保护策略。实际上，需要努力维持这些品种的遗传多样性。改善这些品种中记录和监测近交的系统可能有助于它们的就地保护，考虑到这一点，基因组数据的可用性是一个基本资源。
