Estimation of DNA sequence diversity in bovine cytokine genes

DNA sequence variation provides the fundamental material for improving live stock through selection. In cattle, single nucleotide polymorphisms and sma ll insertions/deletions (collectively referred to here as SNPs) have been i dentified in cytokine genes and scored in a reference population to determi ne linkage map positions. The aim of the present study was twofold: 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 commerci al populations. Forty-dye SNP markers in DNA segments from nine cytokine ge ne loci were analyzed in 26 reference parents. Comparison of all 52 haploid genomes at each PCR amplicon locus revealed an average of one SNP per 143 bp of sequence, whereas comparison of any two chromosomes identified hetero zygous sites, on average, every 443 bp. The combination of these 45 SNP gen otypes was sufficient to uniquely identify each of the 26 animals. The aver age number of haplotype alleles (4.4) per PR amplicon (688 bp) and the perc entage heterozygosity among founding parents (50%) were similar to those fo r microsatellite markers in the same population. For 49 sires from seven co mmon breeds of beef cattle, SNP genotypes (1225 total) were obtained by mat rix-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 g enotypes. The latter allows a wide range of genetic studies in commercial p opulations of cattle where genotypic information from relatives may not be available.