Rapid identification of single nucleotide polymorphisms and estimation of allele frequencies using sequence traces from DNA pools
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The Department of Animal Science originally concerned itself with teaching the selection, breeding, feeding and care of livestock. Today it continues this study of the symbiotic relationship between animals and humans, with practical focuses on agribusiness, science, and animal management.
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The Department of Animal Husbandry was established in 1898. The name of the department was changed to the Department of Animal Science in 1962. The Department of Poultry Science was merged into the department in 1971.
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- Department of Animal Husbandry (1898–1962)
- College of Agricultural and Life Sciences (parent college)
- Department of Poultry Science (merged with, 1971)
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Abstract
Millions of single nucleotide polymorphisms (SNP) are now known in the chicken, but the ones that segregate may differ among populations. The current study characterized a simple method to simultaneously identify SNP in populations and to estimate allele frequencies by using relative peak heights of nucleotides in sequencing traces from DNA pools. In the first experiment, known concentration gradients of alleles were produced by measured admixture of DNA from highly inbred individual chickens. In the second experiment, pools of DNA from 100 individuals of each of 3 populations were produced, and the estimated frequencies were compared with those from genotyping of individuals sampled from the same populations. Linear relationships (slope = 0.93 to 1.02) were demonstrated between relative peak heights of nucleotide sequence traces and allelic frequency from both types of experimental samples. The correlation of frequency estimates from pools and individual genotyping was 0.917 to 0.997. Therefore, relative peak heights of nucleotides in sequence traces from DNA isolated from blood pools provide accurate estimates of SNP frequencies of the population from which the pool individuals were sampled and can, therefore, increase efficiency of selecting SNP to genotype in specific populations.
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This article is published as Ye, X., S. McLeod, D. Elfick, J. C. Dekkers, and S. J. Lamont. "Rapid identification of single nucleotide polymorphisms and estimation of allele frequencies using sequence traces from DNA pools." Poultry Science 85, no. 7 (2006): 1165-1168. DOI: 10.1093/ps/85.7.1165. Posted with permission.