Estimation of DNA sequence diversity in bovine cytokine genes
Estimation of DNA sequence diversity in bovine cytokine genes
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DOI：
10.1007/s003350010223
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发表时间：
2001-01-01
期刊：
影响因子：
2.5
通讯作者：
Laegreid, WW
中科院分区：
文献类型：
--
作者：
Heaton, MP;Grosse, WM;Laegreid, WW
DNA序列变异为通过选择改良家畜提供了基础材料。在牛中，单核苷酸多态性和小插入/缺失（在此统称为SNP）已在细胞因子基因中鉴定，并在参考群体中评分以确定连锁图谱位置。本研究的目的是双重的：第一，估计SNP的频率在参考人群的肉牛，第二，以确定细胞因子单倍型在一组从商业人口的公牛。在26个参考亲本中分析了来自9个细胞因子基因位点的DNA片段中的40个染料SNP标记。在每个PCR扩增子基因座处的所有52个单倍体基因组的比较揭示了平均每143 bp序列一个SNP，而任何两个染色体的比较鉴定了杂合位点，平均每443 bp。这45种SNP基因型的组合足以唯一地鉴定26只动物中的每一只。每个PR扩增子（688 bp）的平均单倍型等位基因数（4.4）和创始父母（50%）之间的杂合性百分比相似的微卫星标记在同一群体中。从7个常见品种的肉牛，49公牛，SNP基因型（共1225）获得的基质辅助激光解吸/电离飞行时间质谱（MALDI-TOF MS）在3个扩增子位点。在不使用亲本或子代基因型的情况下，正确推导出每个父系的所有三种扩增子单倍型。后者允许在商业牛种群中进行广泛的遗传研究，其中可能无法获得亲属的基因型信息。
DNA sequence variation provides the fundamental material for improving livestock through selection. In cattle, single nucleotide polymorphisms and small insertions/deletions (collectively referred to here as SNPs) have been identified in cytokine genes and scored in a reference population to determine 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 commercial populations. Forty-dye SNP markers in DNA segments from nine cytokine gene 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 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 PR amplicon (688 bp) and the percentage 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 genotypes (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 allows a wide range of genetic studies in commercial populations of cattle where genotypic information from relatives may not be available.