Davies Livestock Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Adelaide, SA 5371, Australia.
MGI Australia Pty Ltd., Brisbane, QLD 4000, Australia.
Genes (Basel). 2024 Sep 18;15(9):1218. doi: 10.3390/genes15091218.
(1) Background: Target capture sequencing (TCS) is potentially a cost-effective way to detect single-nucleotide polymorphisms (SNPs) and an alternative to SNP array-based genotyping. (2) Methods: We evaluated the effectiveness and reliability of TCS in cattle breeding scenarios using 48 female and 8 male samples. DNA was extracted from blood samples, targeted for 71,746 SNPs with TWIST probes, and sequenced on an MGI platform. GATK and BCFtools were evaluated for the best genotyping calling tool. The genotypes were compared to existing genotypes from the Versa50K SNP array of the same animals by measuring accuracy as concordance (%) and R. (3) Results: In this study, 71,553 SNPs and 166 indels were identified. The genotype comparison of 37,130 common SNPs between TCS and SNP arrays yielded high agreement, with a mean concordance of 98%, R of 0.98 and Cohen's kappa of 0.97. The concordances of sex prediction, parent verification and validation of five genotype markers of interest important for Wagyu breeding were 100% between TCS and SNP array. The elements of the genomic relationship matrix (GRM) constructed from the SNP array and TCS data demonstrated a correlation coefficient approaching unity (r = 0.9998). (4) Conclusions: Compared to the SNP array, TCS is a comparable, cost-effective and flexible platform for genotyping SNPs, including non-model organisms and underrepresented commercial animal populations.
(1) 背景：目标捕获测序（TCS）是一种检测单核苷酸多态性（SNP）的具有成本效益的方法，也是基于 SNP 阵列的基因分型的替代方法。(2) 方法：我们使用 48 个雌性和 8 个雄性样本评估了 TCS 在牛育种场景中的有效性和可靠性。从血液样本中提取 DNA，用 TWIST 探针靶向 71746 个 SNP，并在 MGI 平台上进行测序。评估了 GATK 和 BCFtools 作为最佳基因分型调用工具的效果。通过测量一致性（%）和 R 来比较与相同动物的 Versa50K SNP 阵列的现有基因型。(3) 结果：在这项研究中，鉴定出了 71553 个 SNP 和 166 个插入缺失。TCS 和 SNP 阵列之间 37130 个常见 SNP 的基因型比较显示出高度一致性，平均一致性为 98%，R 为 0.98，Cohen's kappa 为 0.97。TCS 和 SNP 阵列之间性别预测、亲本验证和五个对和牛育种重要的感兴趣基因型标记的验证的一致性为 100%。基于 SNP 阵列和 TCS 数据构建的基因组关系矩阵（GRM）的元素显示出接近 1 的相关系数（r = 0.9998）。(4) 结论：与 SNP 阵列相比，TCS 是一种具有成本效益的、灵活的 SNP 基因分型平台，包括非模式生物和代表性不足的商业动物群体。
