Data_Sheet_1_SNP-Based Genotyping Provides Insight Into the West Asian Origin of Russian Local Goats.PDF

Specific local environmental and sociocultural conditions have led to the creation of various goat populations in Russia. National goat diversity includes breeds that have been selected for down and mohair production traits as well as versatile local breeds for which pastoralism is the main management system. Effective preservation and breeding programs for local goat breeds are missing due to the lack of DNA-based data. In this work, we analyzed the genetic diversity and population structure of Russian local goats, including Altai Mountain, Altai White Downy, Dagestan Downy, Dagestan Local, Karachaev, Orenburg, and Soviet Mohair goats, which were genotyped with the Illumina Goat SNP50 BeadChip. In addition, we addressed genetic relationships between local and global goat populations obtained from the AdaptMap project. Russian goats showed a high level of genetic diversity. Although a decrease in historical effective population sizes was revealed, the recent effective population sizes estimated for three generations ago were larger than 100 in all studied populations. The mean runs of homozygosity (ROH) lengths ranged from 79.42 to 183.94 Mb, and the average ROH number varied from 18 to 41. Short ROH segments (<2 Mb) were predominant in all breeds, while the longest ROH class (>16 Mb) was the least frequent. Principal component analysis, Neighbor-Net graph, and Admixture clustering revealed several patterns in Russian local goats. First, a separation of the Karachaev breed from other populations was observed. Moreover, genetic connections between the Orenburg and Altai Mountain breeds were suggested and the Dagestan breeds were found to be admixed with the Soviet Mohair breed. Neighbor-Net analysis and clustering of local and global breeds demonstrated the close genetic relations between Russian local and Turkish breeds that probably resulted from past admixture events through postdomestication routes. Our findings contribute to the understanding of the genetic relationships of goats originating in West Asia and Eurasia and may be used to design breeding programs for local goats to ensure their effective conservation and proper management.

特定的本土环境与社会文化条件，孕育了俄罗斯境内诸多山羊种群。该国山羊遗传多样性既包含针对绒毛与马海毛生产性状选育的专用品种，也涵盖以游牧业为主要管理模式的多用途地方品种。由于缺乏基于DNA的遗传数据，目前尚未建立针对本土山羊品种的有效保护与选育计划。本研究对俄罗斯本土山羊的遗传多样性与种群结构进行了分析，涉及阿尔泰山地山羊、阿尔泰白绒山羊、达吉斯坦绒山羊、达吉斯坦本地山羊、卡拉恰伊山羊、奥伦堡山羊以及苏联马海毛山羊，所有受试个体均使用Illumina山羊SNP50基因分型芯片（Illumina Goat SNP50 BeadChip）完成基因分型。此外，本研究还分析了从AdaptMap项目（AdaptMap project）获取的全球山羊种群与俄罗斯本土山羊种群间的遗传亲缘关系。俄罗斯山羊整体展现出较高的遗传多样性水平，尽管研究发现其历史有效种群规模有所下降，但针对所有受试种群估算的近三代有效种群规模均大于100。纯合子片段（runs of homozygosity, ROH）的平均长度区间为79.42至183.94 Mb，平均ROH数量则介于18至41之间；短片段ROH（<2 Mb）在所有品种中均占主导地位，而最长ROH类别（>16 Mb）的出现频率最低。主成分分析（Principal Component Analysis）、邻网图（Neighbor-Net graph）构建以及Admixture群体混合聚类分析（Admixture clustering）揭示了俄罗斯本土山羊的多种遗传分化模式：具体而言，卡拉恰伊山羊品种与其他种群呈现出明显的遗传分离；此外，奥伦堡山羊与阿尔泰山地山羊之间存在密切的遗传联系，而达吉斯坦山羊类群则与苏联马海毛山羊存在遗传混合现象。邻网图分析与全球、本土山羊种群的聚类结果显示，俄罗斯本土山羊与土耳其山羊种群间存在紧密的遗传亲缘关系，这一现象可能源于驯化后阶段通过多种途径发生的历史遗传混合事件。本研究结果有助于深化对起源于西亚与欧亚大陆的山羊种群遗传亲缘关系的认知，同时可为本土山羊的选育计划制定提供依据，以实现其有效保护与科学管理。