Polymorphism and differentiation indices preferred for genetic analysis among cattle, goats, and sheep

摘要

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 (r of -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).