Identification of divergently selected regions between Japanese Black and Holstein cattle using bovine 50k SNP array
Identification of divergently selected regions between Japanese Black and Holstein cattle using bovine 50k SNP array
复制标题
使用牛 50k SNP 阵列鉴定日本黑牛和荷斯坦牛之间的不同选择区域
DOI：
10.1111/j.1740-0929.2011.00927.x
复制
发表时间：
2012
影响因子：
2
通讯作者：
Mannen H
中科院分区：
文献类型：
--
作者：
Hosokawa D;Ishii A;Yama j i K;Sasazaki S;Oyama K;Mannen H
与性状相关的基因的平均等位基因频率之间的差异表明，这将是人为选择的证据。滑动窗口法是一种有效的方法，以确定基因组区域已在两个品种之间的差异选择。本研究的目的是根据通过高密度单核苷酸多态性（SNP）面板获得的基因型信息，确定日本黑牛（JB）和日本荷斯坦牛（JH）之间的差异选择区域。在对100头牛（50头JB和50头JH）的54 001个SNP标记进行基因分型后，共获得40 635个SNP位点。 对于这些SNP中的每一个，计算JB和JH的等位基因频率之间的绝对差异。在本研究中，10个连续的SNP被定义为窗口的组成部分。对于每个窗口，计算等位基因频率的平均差异。这被称为滑动窗口平均差（SWAD）。在40 055个窗口中，我们重点关注了39个SWAD最大的窗口。 这相当于所有窗口的0.1%，SWAD大于0.435。其中一些窗口相互重叠，分布在11个区域。这些区域与已报道的数量性状基因座一致性较好，因此可能是选择标记和携带致病突变的良好候选者。
Differences between average allelic frequencies of genes that relate to traits suggest that it would be evidence of artificial selections. Sliding window approach is a useful method to identify genomic regions that have been differently selected between two breeds. The objective of this study was to identify the divergently selected regions between Japanese Black (JB) and Japanese Holstein (JH) cattle based on genotypic information obtained through a high‐density single nucleotide polymorphism (SNP) panel. After genotyping of 54 001 SNP markers on 100 animals (50 JB and 50 JH), 40 635 SNPs were suitable for the analysis. For each of these SNPs, the absolute difference between allelic frequencies of JB and JH was calculated. In the current study, 10 consecutive SNPs were defined as components of a window. For each window, the average difference in allelic frequency was calculated. This was termed sliding window average difference (SWAD). Among 40 055 windows, we focused on 39 windows with the largest SWAD. This was equivalent to 0.1% of all windows and the SWAD was more than 0.435. Some of these windows overlapped and were distributed in 11 regions. These regions were in good agreement with reported quantitative trait locus, therefore would be selection signatures and good candidates that harbor the causative mutations.