Abstract
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 (G ST ) and gene differentiation (δ ST ). We found significantly higher correlations (p < 0.001) with other indices for sequence conservation (r of –0.66 to –0.98), θη (0.52–0.95), and γ ST (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).
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Acknowledgments
This work was supported by the National Natural Science Fund of China (No. 31172196) and Provincial Natural Science Fund of Hebei (C2010000775 and C2012204009), the university innovation team leader training program in Hebei Province (LJRC004) and the Earmarked Fund for Hebei Layer Innovation Team of Modern Agro-industry Technology Research System.
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Li, L., Li, X., Zhou, R. et al. Polymorphism and Differentiation Indices Preferred for Genetic Analysis Among Cattle, Goats, and Sheep. Biochem Genet 52, 209–224 (2014). https://doi.org/10.1007/s10528-014-9641-1
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DOI: https://doi.org/10.1007/s10528-014-9641-1