Polymorphism and Differentiation Indices Preferred for Genetic Analysis Among Cattle, Goats, and Sheep

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,...

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Bibliographic Details
Published in:Biochemical genetics 2014-04, Vol.52 (3-4), p.209-224
Main Authors: Li, Lanhui, Li, Xianglong, Zhou, Rongyan, Ren, Yuhong
Format: Article
Language:English
Subjects:
Animals
Biochemistry
Biomedical and Life Sciences
Biomedicine
Cattle
Cattle - genetics
Chromosomes
Cluster Analysis
Conserved Sequence
Gene Flow
Gene Frequency
genes
genetic techniques and protocols
genetic variation
goats
Goats - genetics
Human Genetics
Medical Microbiology
Multigene Family
Polymorphism, Genetic
Principal Component Analysis
sex chromosomes
sheep
Sheep - genetics
Species Specificity
Zoology
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Summary: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).
ISSN:0006-2928
1573-4927
DOI:10.1007/s10528-014-9641-1