Samantha L. Van Buren, Jessica L. Petersen, C. Titus Brown, Carrie J. Finno
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引用次数: 0
Abstract
With advancing genomic technologies, single-nucleotide polymorphism (SNP) arrays and whole genome sequencing (WGS) have become essential tools in equine genetic research. In this study, we assessed the concordance in SNP calls and trait-mapping efficacy by comparing data of 21 horses both genotyped on the Equine 670 K SNP array and sequenced at either ~12× or ~30× depth. Our analysis revealed that higher sequencing depths were significantly associated with fewer discordant calls between platforms. Additionally, we investigated the most frequent no-call and discordant positions and identified positions that were indels or multiallelic in the WGS. To assess the effectiveness of the 670 K SNP array vs. WGS in trait association studies, we mapped the chestnut coat color. Both technologies showed a clear peak at the expected locus, although neither association had loci reaching Bonferroni-corrected statistical significance, which was not statistically possible in this small group of horses. The findings of this study provide valuable insights for making informed decisions when selecting between SNP arrays and WGS at varying sequencing depths for equine genomic research applications.
随着基因组技术的发展,单核苷酸多态性(SNP)阵列和全基因组测序(WGS)已成为马遗传研究的重要工具。在这项研究中,我们通过比较21匹马的数据来评估SNP呼叫的一致性和性状定位效率,这21匹马都在马670 K SNP阵列上进行基因分型,并在~12×或~30×深度进行测序。我们的分析显示,较高的测序深度与平台之间较少的不一致呼叫显着相关。此外,我们调查了WGS中最常见的无召唤和不一致的位置,并确定了索引或多等位基因的位置。为了评估670 K SNP阵列与WGS在性状关联研究中的有效性,我们绘制了栗子毛色图谱。两种技术都在预期位点上显示出明显的峰值,尽管两种关联都没有达到bonferroni校正的统计显著性,这在这一小群马中是不可能的。本研究的发现为在不同测序深度的SNP阵列和WGS之间进行选择时做出明智的决定提供了有价值的见解。
期刊介绍:
Animal Genetics reports frontline research on immunogenetics, molecular genetics and functional genomics of economically important and domesticated animals. Publications include the study of variability at gene and protein levels, mapping of genes, traits and QTLs, associations between genes and traits, genetic diversity, and characterization of gene or protein expression and control related to phenotypic or genetic variation.
The journal publishes full-length articles, short communications and brief notes, as well as commissioned and submitted mini-reviews on issues of interest to Animal Genetics readers.