Polymorphism and Differentiation Indices Preferred for Genetic Analysis Among Cattle, Goats, and Sheep
Polymorphism and Differentiation Indices Preferred for Genetic Analysis Among Cattle, Goats, and Sheep
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DOI：
10.1007/s10528-014-9641-1
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发表时间：
2014-01
影响因子：
2.4
通讯作者：
Lan-hui Li;Xianglong Li;R. Zhou;Y. Ren
中科院分区：
文献类型：
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作者：
Lan-hui Li;Xianglong Li;R. Zhou;Y. Ren
大多数多态性和分化的研究都是基于单个基因；很少有人研究过众多基因之间的差异。通过对牛、山羊和绵羊的1614个序列的保守性、多态性和遗传分化参数的分析，找到了40个基因的优选指数。聚类和主成分因子（PCF）分析显示了三个PCF: PCF1，代表多态性和分化；PCF2，表示核苷酸用法；PCF3分别代表基因流动（GST）和基因分化（δST）。我们发现，序列保守性与其他指数（rof -0.66 ~ -0.98）、θη(0.52 ~ 0.95)和γST（0.54 ~ 0.96）的相关性显著较高（p< 0.001）。这表明它们分别适用于估计基因的保守性、多态性和分化性。常染色体与性染色体的密码子偏倚指数差异有统计学意义（p< 0.01）。
Most studies of polymorphism and differentiation are based on a single gene; few have treated differences among numerous genes. We have analyzed the parameters of conservation, polymorphism, and genetic differentiation to find the preferred index of 40 genes, with 1,614 sequences from cattle, goats, and sheep. Clustering and principal component factor (PCF) analyses revealed three PCFs: PCF1, representing polymorphism and differentiation; PCF2, representing nucleotide usage; and PCF3, representing gene flow (GST) and gene differentiation (δST). We found significantly higher correlations (p< 0.001) with other indices for sequence conservation (rof –0.66 to –0.98), θη (0.52–0.95), and γST(0.54–0.96). This shows that they are preferable for estimating conservation, polymorphism, and differentiation of genes, respectively. The codon bias index was significantly different between the autosome and sex chromosomes (p< 0.01).