使用从猪的全基因组序列数据中预选标记物的多线 ssGBLUP 评估
Sungbong Jang1, Roger Ros-Freixedes2, John M Hickey3
1Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States.
Frontiers in genetics
|May 30, 2023
概括
使用全基因组测序 (WGS) 数据对猪的多线基因组评估 (MLE) 对预测准确性的好处有限. 考虑到几何系之间的遗传差异对于可比结果至关重要,但预先选择的变体并没有显著提高性能.
科学领域:
- 动物遗传学动物遗传学
- 量化遗传学 量化遗传学
- 基因组预测 基因组预测
背景情况:
- 通过将多线数据与全基因组测序 (WGS) 集成,可以增强猪的基因组评估.
- 需要大规模的数据来捕捉种群变异性,以便进行有效的基因组评估.
研究的目的:
- 在多线基因组评估 (MLE) 中研究结合不同终端猪系的大规模数据的策略.
- 在单步GBLUP (ssGBLUP) 模型中评估从WGS数据中预选的变体的实用性.
主要方法:
- 采用单步 GBLUP (ssGBLUP) 模型进行多线基因组评估 (MLE) 在三个终端猪系的五个特征中.
- 探索未知家长群 (UPG) 和元创始人 (MF) 来管理线条之间的遗传差异.
- 预先选择的序列变体使用多线基因组范围的关联研究 (GWAS) 或链接不平衡 (LD) 修剪.
主要成果:
- 使用UPG和MF的多线基因组评估 (MLE) 与单线评估 (SLE) 相比,预测准确度的增长很小或没有.
- 将GWAS的预选变体纳入商业SNP芯片,在特定线路中,平均每日料摄入量的最大精度增加了0.02.
- 在MLE中使用预选序列变异没有观察到任何好处,BayesR权重也没有改善ssGBLUP的性能.
结论:
- 在使用预选的全基因组序列变异用于猪中MLE时,即使具有大量的归算序列数据,也发现了有限的益处.
- 准确计算线路差异对于MLE来说至关重要,以实现与SLE可比的预测.
- MLE的主要好处是能够在不同的猪系中进行可比的预测.
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