Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Via Santa Sofia 100, 95123, Catania, Italy.
Dipartimento Scienze Agrarie e Ambientali, Produzione, Territorio, Agroenergia, University of Milan, Via Giovanni Celoria 2, 20133, Milan, Italy.
Sci Rep. 2024 Jan 2;14(1):3. doi: 10.1038/s41598-023-49125-x.
Heterozygosity-rich regions (HRR) are genomic regions of high heterozygosity, which may harbor loci related to key functional traits such as immune response, survival rate, fertility, and other fitness traits. This study considered 30 Italian and 19 worldwide goat breeds genotyped with the Illumina GoatSNP50k BeadChip. The aim of the work was to study inter-breed relationships and HRR patterns using Sliding Window (SW) and Consecutive Runs (CR) detection methods. Genetic relationships highlighted a clear separation between non-European and European breeds, as well as the north-south geographic cline within the latter. The Pearson correlation coefficients between the descriptive HRR parameters obtained with the SW and CR methods were higher than 0.9. A total of 166 HRR islands were detected. CHI1, CHI11, CHI12 and CHI18 were the chromosomes harboring the highest number of HRR islands. The genes annotated in the islands were linked to various factors such as productive, reproductive, immune, and environmental adaptation mechanisms. Notably, the Montecristo feral goat showed the highest number of HRR islands despite the high level of inbreeding, underlining potential balancing selection events characterizing its evolutionary history. Identifying a species-specific HRR pattern could provide a clearer view of the mechanisms regulating the genome modelling following anthropogenic selection combined with environmental interaction.
高杂合区域（HRR）是高度杂合的基因组区域，可能包含与免疫反应、存活率、生育率和其他适应性状等关键功能性状相关的基因座。本研究考虑了 30 个意大利和 19 个全球山羊品种，这些品种均使用 Illumina GoatSNP50k BeadChip 进行了基因分型。该研究的目的是使用滑动窗口（SW）和连续运行（CR）检测方法研究品种间的关系和 HRR 模式。遗传关系清楚地区分了非欧洲和欧洲品种，以及后者的南北地理梯度。SW 和 CR 方法获得的描述性 HRR 参数之间的 Pearson 相关系数高于 0.9。共检测到 166 个 HRR 岛。CHI1、CHI11、CHI12 和 CHI18 是包含最多 HRR 岛的染色体。注释在岛屿中的基因与各种因素有关，如生产、生殖、免疫和环境适应机制。值得注意的是，尽管 Montecristo 野生山羊存在高度的近亲繁殖，但它具有最高数量的 HRR 岛，这表明其进化历史可能存在潜在的平衡选择事件。确定物种特异性的 HRR 模式可以更清楚地了解调节基因组建模的机制，这些机制与人为选择结合环境相互作用有关。
