Identification of genomic regions associated with differences in fleece type in Huacaya and Suri alpacas (Vicugna pacos)

IF 16.4 1区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY
K. Tan, O. O. Adeniyi, A. Letko, G. RuddGarces, E. Manz, H. Wagner, P. Zanolari, C. Drögemüller, G. Lühken
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Abstract

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.

Abstract Image

华卡亚羊驼和苏里羊驼羊毛类型差异相关基因组区域的鉴定。
羊毛类型的差异是华卡亚羊驼和苏里羊驼两种羊驼的显著特征。苏里绒型比华卡雅型遗传优势,导致后代具有苏里表型。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。本研究利用76k羊驼SNP阵列对来自德国和瑞士的91头羊驼(54头华卡亚羊驼和37头苏利羊驼)进行了基因分型。只有59k个染色体定位标记与羊驼参考组合VicPac3.1相对应,经过质量控制后,保留49866个snp用于群体结构评估和全基因组关联研究。主成分分析和邻居连接树分析表明,两个羊毛型队列重叠,而不是形成两个不同的集群。在16号染色体支架区(NW_021964192.1)发现了全基因组显著相关的标记,该区域含有一簇角蛋白基因。在苏瑞羊驼中发现的一种单倍型已被确定,它支持显性遗传。在0.4 Mb的临界区间内,对9只全基因组测序的两种羊毛类型的羊驼进行变异过滤,没有发现两种羊毛类型的特定变异完全分离。据我们所知,这是首次使用最近开发的物种特异性SNP阵列来鉴定与羊驼羊毛类型差异相关的基因组区域的研究。目前还存在一些局限性,如参考装配体的初步状态和羊驼基因组的不完整注释等。
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来源期刊
Accounts of Chemical Research
Accounts of Chemical Research 化学-化学综合
CiteScore
31.40
自引率
1.10%
发文量
312
审稿时长
2 months
期刊介绍: Accounts of Chemical Research presents short, concise and critical articles offering easy-to-read overviews of basic research and applications in all areas of chemistry and biochemistry. These short reviews focus on research from the author’s own laboratory and are designed to teach the reader about a research project. In addition, Accounts of Chemical Research publishes commentaries that give an informed opinion on a current research problem. Special Issues online are devoted to a single topic of unusual activity and significance. Accounts of Chemical Research replaces the traditional article abstract with an article "Conspectus." These entries synopsize the research affording the reader a closer look at the content and significance of an article. Through this provision of a more detailed description of the article contents, the Conspectus enhances the article's discoverability by search engines and the exposure for the research.
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