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在四个意大利绵羊品种中,使用SNP数据进行微卫星归算,用于亲属验证

Michela Ablondi¹, Giorgia Stocco¹, Matteo Cortellari²

¹Department of Veterinary Science, Università degli studi di Parma, Parma, Italy.

Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie

|December 7, 2023

概括

这项研究开发了一个微卫星 (MS) 归算管道从单核酸多态 (SNP) 数据用于羊亲属测试. 该管道实现了超过94%的一致性,即使使用混合基因型平台,也可以实现准确的亲属验证.

科学领域:

基因组学就是基因组学.
动物遗传学动物遗传学
生物信息学是一种生物信息学.

背景情况:

微卫星 (MS) 标记器传统上用于牲畜亲属验证,因为其高多态性.
基因组时代引入了单核酸多态性 (SNP) 标记,提供了成本和自动化优势,但对亲属测试的过渡速度很慢.
一个关键的挑战是缺少一个统一的基因型识别平台的父母和后代,阻碍SNP采用亲属验证.

研究的目的:

评估微卫星 (MS) 归算管道的可行性,使用四种本土意大利奶羊品种的单核酸多态 (SNP) 数据.
克服基因型化成本障碍,并在从MS转向SNP标记器的过渡过程中实现亲属验证.
评估从SNP中归算MS的准确性和实际优势,用于羊的亲属测试.

主要方法:

开发并实施了一个MS归算管道,使用来自11个MS的SNP数据和四种羊品种 (Comisana,Massese,Delle Langhe,Sarda) 的Ovine SNP50珠芯片.
在每个成员国的2Mb窗口内对标记器和选定的SNP进行质量控制.
该管道涉及存储VCF格式的数据,掩盖10%个人的MS数据,并使用归算程序从剩余90%的MS中归算掩盖的MS.

主要成果:

经过质量控制,使用了8个成员国和505个SNP (每个成员国平均63个SNP).
在MS的归算管道中,在所有品种和分析类型中,总体一致率超过94%,但不包括表现最低的MS (OARAE129).
与MS的原始数据相比,在94%的案例中,归算的MS数据导致了同等的亲属关系验证结果.

结论:

从SNP开发的MS归算管道是可行的,并展示了用于羊亲属身份验证的实际优势.
这种方法有效地弥合了传统成员国和新兴SNP基因型化平台之间的差距.
高一致率表明在绵羊中进行亲属测试是一种可靠的方法,这有助于采用基因组工具.

关键词:

归算是指指责一个人.当地的品种,当地品种.微卫星是微卫星中的一个.亲属关系测试亲属关系测试单核酸多形态的单核酸多形态

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