Application of mathematical expectation (ME) strategy for detecting low frequency mutations: An example for evaluating 14-bp insertion/deletion (indel) within the bovine PRNP gene
Application of mathematical expectation (ME) strategy for detecting low frequency mutations: An example for evaluating 14-bp insertion/deletion (indel) within the bovine PRNP gene
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DOI：
10.1080/19336896.2016.1211593
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发表时间：
2016-08
期刊：
影响因子：
2.3
通讯作者：
Qing Yang;Sihuan Zhang;Liangliang Liu;Xiu-Kai Cao;C. Lei;Xinglei Qi;Fengpeng Lin;Weidong Qu;Xingshan Qi;Jiming Liu;Rongmin Wang;Hong Chen;X. Lan
中科院分区：
文献类型：
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作者：
Qing Yang;Sihuan Zhang;Liangliang Liu;Xiu-Kai Cao;C. Lei;Xinglei Qi;Fengpeng Lin;Weidong Qu;Xingshan Qi;Jiming Liu;Rongmin Wang;Hong Chen;X. Lan
摘要基于数学期望（ME）策略的检测方法对于大样本的低频突变筛查具有快速、准确的特点。已有研究发现，牛PRNP基因3′非翻译区（3′ UTR）14 bp插入/缺失（indel）变异在中国以外的世界牛种中出现频率较低（≤5%），而在中国牛种中尚未发现。因此，本研究旨在鉴定中国5个主要地方黄牛品种PRNP基因内14 bp的indel，并分析其与表型性状的相关性。首次采用ME策略检测了低频率indel多态性，发现秦川、咸安、南阳、佳县和吉安的次要等位基因频率分别为0.038、0.033、0.013、0.003和0。与传统的逐个样品筛选的检测方法相比，ME法的反应时间分别减少了62.5%、64.9%、77.6%、88.9%和66.4%。此外，该14 bp indel与秦川牛的体长、夏南牛的体重和腰围等生长性状显著相关。本研究结果表明，基于ME策略的方法能够快速、可靠、经济地检测出低频率突变，为肉牛标记辅助选择（MAS）提供了有价值的理论依据。
ABSTRACT The detection method based on the mathematical expectation (ME) strategy is fast and accuracy for low frequency mutation screening in large samples. Previous studies have found that the 14-bp insertion/deletion (indel) variants of the 3′ untranslated region (3′ UTR) within bovine PRNP gene have been characterized with low frequency (≤5%) in global breeds outside China, which has not been determined in Chinese cattle breeds yet. Therefore, this study aimed to identify the 14-bp indel within PRNP gene in 5 major Chinese indigenous cattle breeds and to evaluate its associations with phenotypic traits. It was the first time to use ME strategy to detect low frequency indel polymorphisms and found that minor allele frequency was 0.038 (Qinchuan), 0.033 (Xianan), 0.013 (Nanyang), 0.003 (Jiaxian), and zero (Ji'an), respectively. Compared to the traditional detection method by which the sample was screened one by one, the reaction time by using the ME method was decreased 62.5%, 64.9%, 77.6%, 88.9% and 66.4%, respectively. In addition, the 14-bp indel was significantly associated with the growth traits in 2 cattle breeds, with the body length of Qinchuan cattle as well as the body weight and waistline of Xianan cattle. Our results have uncovered that the method based on ME strategy is rapid, reliable, and cost-effective for detecting the low frequency mutation as well as our findings provide a potential valuable theoretical basis for the marker-assisted selection (MAS) in beef cattle.