The difference in fleece type is the distinguishing trait between the two types of alpacas (Vicugna pacos), Huacaya and Suri. The Suri fleece type has been found to be inherited dominantly over the Huacaya type, resulting in offspring with the Suri phenotype. The aim of our study was to map genomic regions associated with the two different fleece types. In this study, 91 alpacas (54 Huacayas and 37 Suris) from Germany and Switzerland were genotyped using the 76k alpaca SNP array. Only 59k chromosome-localised markers map to the alpaca reference assembly VicPac3.1, and after quality control 49 866 SNPs, were retained for population structure assessment and to conduct a genome-wide association study. Both principal component and neighbour-joining tree analysis showed that the two fleece-type cohorts overlapped rather than forming two distinct clusters. Genome-wide significantly associated markers were observed in the scaffold region of chromosome 16 (NW_021964192.1), which contains a cluster of keratin genes. A haplotype predominantly found in Suri alpacas has been identified which supports dominant inheritance. Variant filtering of nine whole-genome sequenced alpacas from both fleece types in the critical interval of 0.4 Mb did not reveal perfect segregation of either fleece type for specific variants. To our knowledge, this is the first study to use the recently developed species-specific SNP array to identify genomic regions associated with differences in fleece type in alpacas. There are still some limitations, such as the preliminary status of the reference assembly and the incomplete annotation of the alpaca genome.

中文翻译：

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鉴定与华卡亚羊驼和苏里羊驼 (Vicugna pacos) 羊毛类型差异相关的基因组区域

羊毛类型的差异是两种羊驼（Vicugna pacos）Huacaya 和 Suri 之间的区别特征。已发现 Suri 羊毛类型比 Huacaya 类型具有显性遗传，从而产生具有 Suri 表型的后代。我们研究的目的是绘制与两种不同羊毛类型相关的基因组区域图。在这项研究中，使用 76k 羊驼 SNP 芯片对来自德国和瑞士的 91 只羊驼（54 只 Huacayas 和 37 只 Suris）进行了基因分型。仅将 59k 染色体定位标记映射到羊驼参考装配体 VicPac3.1，并在质量控制后保留 49 866 个 SNP，用于群体结构评估和进行全基因组关联研究。主成分和邻接树分析都表明，两个羊毛型群体重叠，而不是形成两个不同的簇。在 16 号染色体的支架区域 (NW_021964192.1) 中观察到全基因组显着相关的标记，该区域包含一组角蛋白基因。已鉴定出主要在苏里羊驼中发现的单倍型，该单倍型支持显性遗传。在 0.4 Mb 的临界区间内，对两种羊毛类型中的 9 只全基因组测序羊驼进行变异过滤，并未揭示任一羊毛类型的特定变异的完美分离。据我们所知，这是第一项使用最近开发的物种特异性 SNP 阵列来识别与羊驼羊毛类型差异相关的基因组区域的研究。目前仍存在一些局限性，例如参考组装的初步状态以及羊驼基因组的注释不完整。