基于DNA池测序法筛选奶牛高信息量SNP标记的可行性

doi:10.3724/SP.J.1005.2014.0691

遗传 ›› 2014, Vol. 36 ›› Issue (7): 691-696.doi: 10.3724/SP.J.1005.2014.0691

基于DNA池测序法筛选奶牛高信息量SNP标记的可行性

初芹¹, 李东², 侯诗宇³, 石万海⁴, 刘林⁴, 王雅春²

1. 北京市农林科学院畜牧兽医研究所, 北京 100097;
2. 中国农业大学动物科技学院, 畜禽育种国家工程实验室, 北京 100193;
3. 鞍山恒利奶牛场, 辽宁 114200;
4. 北京奶牛中心, 北京 100192

收稿日期:2013-12-04 出版日期:2014-07-20 发布日期:2014-06-23
通讯作者: 王雅春, 博士, 副教授, 研究方向：动物遗传育种与分子数量遗传学。E-mail: wangyachun@cau.edu.cn
作者简介:初芹, 博士, 副研究员, 研究方向：动物遗传育种。E-mail: chuqinsd@163.com
基金资助:
国家科技攻关计划项目(编号：2011BAD28B02), 现代农业产业技术体系专项资金(编号：CARS-37), 长江学者与创新团队发展计划项目(编号：IRT1191)和国家自然科学基金项目(编号：31172191)资助

Direct sequencing of DNA pooling for screening highly informative SNPs in dairy cattle

Qin Chu¹, Dong Li², Shiyu Hou³, Wanhai Shi⁴, Lin Liu⁴, Yachun Wang²

1. Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China;
2. Key Laboratory of Agricultural Animal and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China;
3. Anshan Hengli Dairy Cattle Farm, Liaoning 114200, China;
4. Beijing Dairy Cattle Center, Beijing 100192, China

Received:2013-12-04 Online:2014-07-20 Published:2014-06-23

摘要/Abstract

摘要： 首先选择139个牛SNP标记, 利用DNA池测序法, 根据测序峰图中不同碱基信号峰高的比值确定了92个SNP为高信息量标记(比值>1/2); 为了进一步验证筛选的准确性, 对其中59个标记采用基质辅助激光解析电离飞行时间质谱(Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry, MALDI-TOF MS)技术检测了122头荷斯坦牛的基因型。结果显示, 检出率高于85%的标记有56个, 其平均最小等位基因频率(Minor allele frequency, MAF)为0.41, 最小值为0.27, 最大值为0.5; MAF>0.3的标记有54个, 占96.4%(54/56)。文章结果表明, 采用DNA池测序法筛选高信息量SNP标记是可行和可信的。

关键词: 奶牛, DNA池, SNP标记, 基质辅助激光解析电离飞行时间质谱技术, 最小等位基因频率

Abstract: In this study, 139 bovine single nuclear polymorphisms (SNPs) were firstly selected and then directly sequenced using DNA pooling. Based on the ratio of two signal peak values, 92 SNPs with the ratio over 1/2 were considered as potential highly informative markers. To further verify the reliability of screening system, 59 SNP markers were genotyped in 122 Holstein cattle using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) method. The results showed that 56 SNPs had a call rate higher than 85%. The minor allele frequency (MAF) of these 56 markers ranged from 0.27 to 0.5, with an average of 0.41; and in which 54 markers had a MAF over 0.3, covering 96.4% of this group of markers (54/56). Our findings indicate that direct sequencing of DNA pooling is a useful and efficient tool for identifying highly informative SNPs.

Key words: dairy cattle, DNA pooling, single nuclear polymorphism, matrix-assisted laser desorption/ionisation time-of- flight mass spectrometry (MALDI-TOF MS), minor allele frequency

初芹, 李东, 侯诗宇, 石万海, 刘林, 王雅春. 基于DNA池测序法筛选奶牛高信息量SNP标记的可行性[J]. 遗传, 2014, 36(7): 691-696.

Qin Chu, Dong Li, Shiyu Hou, Wanhai Shi, Lin Liu, Yachun Wang. Direct sequencing of DNA pooling for screening highly informative SNPs in dairy cattle[J]. HEREDITAS(Beijing), 2014, 36(7): 691-696.

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基于DNA池测序法筛选奶牛高信息量SNP标记的可行性

Direct sequencing of DNA pooling for screening highly informative SNPs in dairy cattle

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