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评估目标捕获测序对牛基因定型的有效性

Yan Ren¹, Mehar S Khatkar¹, Callum MacPhillamy¹

¹Davies Livestock Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Adelaide, SA 5371, Australia.

|September 28, 2024

概括

目标捕获测序 (TCS) 提供了一种具有成本效益和可靠的方法,用于在牛养殖中进行单核酸多态 (SNP) 基因定型. 与传统的SNP数组相比,这种方法显示出高精度和一致性,使其成为灵活的替代方案.

科学领域:

动物基因组学动物基因组学
分子生物学分子生物学
生物信息学是一种生物信息学.

背景情况:

目标捕获测序 (TCS) 是SNP阵列基因型化的一个潜在的成本效益替代方案.
评估TCS的有效性和可靠性对于其在动物育种中的采用至关重要.

研究的目的:

评估TCS在牛养殖中SNP基因定型的准确性和可靠性.
将TCS性能与已建立的SNP阵列方法进行比较.

主要方法:

来自牛样本的DNA经过了针对71746个SNP的向测序,使用MGI平台上的TWIST探针.
基因型确切性通过比较TCS数据与现有的SNP阵列基因型来评估,测量一致性和R2.
评估了GATK和BCF工具的最佳基因型定型.

主要成果:

对于37,130个常见的SNP,在TCS和SNP数组之间观察到很高的一致性 (平均一致性98%,R2 0.98).
在性别预测,家长验证和关键的Wagyu繁殖标记方面实现了100%的一致性.
从这两种方法构建的基因组关系矩阵显示出强烈的相关性 (r = 0.9998).

结论:

TCS是一种可比,具有成本效益和灵活的SNP牛基因定型平台.
TCS适用于非模型生物和代表性不足的商业动物种群.
这项研究验证了TCS作为动物育种中基因组应用的可靠工具.

关键词:

动物育种动物育种这里是牛群.液体探测器探测器是什么有针对性的捕获序列.

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