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Title: ESTIMATION OF DNA SEQUENCE DIVERSITY IN BOVINE CYTOKINE GENES

Author
item Heaton, Michael - Mike
item Grosse, William
item Kappes, Steven - Steve
item Keele, John
item Chitko-Mckown, Carol
item Cundiff, Larry
item BRAUN, ANDREAS - SEQUENOM, INC.
item LITTLE, DANIEL - SEQUENOM, INC.
item Laegreid, William

Submitted to: Mammalian Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/14/2000
Publication Date: 1/1/2001
Citation: Heaton, M.P., Grosse, W.M., Kappes, S.M., Keele, J.W., Chitko Mckown, C.G., Cundiff, L.V., Braun, A., Little, D.P., Laegreid, W.W. 2001. Estimation of DNA sequence diversity in bovine cytokine genes. Mammalian Genome. 12:32-37.

Interpretive Summary: DNA sequence variation provides the fundamental material for improving livestock through selection. The aim of the present study was two-fold: first, to estimate the DNA sequence variation in a reference population of beef cattle and second, to use that information for determining the genetic types of a group of sires from commercial populations. The DNA sequence diversity was determined by sequence comparison of nine different cytokine genes in 26 different reference cattle. The single nucleotide polymorphisms (SNPS) were then scored in commercial cattle by automated matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). All 49 of the commercial cattle were correctly typed without the use of genetic information from parents or offspring. This enables a wide range of genetic studies in commercial populations of cattle where genotype information from relatives may not be available.

Technical Abstract: DNA sequence variation provides the fundamental material for improving livestock through selection. In cattle, single nucleotide polymorphisms and small insertion/deletions have been identified in cytokine genes and scored in a reference population to determine linkage map position and, thereby, integrate the bovine and human maps. The aim of the present study ywas two-fold: first, to estimate the SNP frequency in a reference population of beef cattle and second, to determine cytokine haplotypes in a group of sires from commercial populations. Forty-five SNP markers at nine cytokine gene loci were analyzed in 26 reference parents. Comparison of all 52 chromosomes at each PCR amplicon locus revealed an average of one SNP per 143 bp of sequence, whereas, comparison of any two chromosomes identified heterozygous sites, on average, every 443 bp. The combination of these 45 SNP genotypes was sufficient to uniquely identify each of the 26 animals. The average number of haplotype alleles (4.4) per PCR amplico (688 bp) and the percent heterozygosity among founding parents (50%) were similar to those for microsatellite markers in the same population. For 49 sires from seven common breeds of beef cattle, SNP genotype (1225 total) were obtained by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) at three amplicon loci. All three of the amplicon haplotypes were correctly deduced for each sire without the use of parent or progeny genotypes. The latter enables a wide range of genetic studies in commercial populations of cattle where genotypic information from relatives may not be available.