Animal Improvement Programs Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350, USA.
J Dairy Sci. 2013 Mar;96(3):1874-9. doi: 10.3168/jds.2012-6176. Epub 2013 Jan 16.
Selection, mating, and improvement of dairy animals have required accurate pedigrees. Genomic tools allow paternal ancestors to be easily confirmed or discovered because most sires are genotyped for many markers, but maternal ancestors are more difficult to discover because most female ancestors are not genotyped. Three methods to discover maternal grandsires (MGS) were developed and compared. Conflicts were counted one single nucleotide polymorphism (SNP) at a time between genotypes of the animal and potential MGS (duo method) or also using the sire's genotype (trio method). Alternatively, haplotypes of a potential MGS were matched to the animal's maternal haplotype, obtained by using linkage across loci (HAP method). The duo and trio methods can be performed as soon as a genotype is received because no imputation is required. The HAP method improved accuracy because genotypes with 2,683 (3 K) SNP were imputed to the 45,187 (50K) SNP used for genomic evaluation. The HAP method was tested using modified pedigrees with 5% of true MGS replaced by a random genotyped bull from the same birth year and 5% of MGS set to missing for 4,134 Holsteins, 552 Jerseys, and 142 Brown Swiss that had confirmed, genotyped sires. Those same animals were used to test the duo and trio methods, except that some animals had multiple genotypes and imputed dams were excluded. Accuracy measured how often the correct MGS was selected from among 12,152 genotyped Holstein, 2,265 Jersey, and 1,605 Brown Swiss potential MGS. Accuracies were 61, 60, and 65%, respectively, with the duo method; 95, 91, and 94% with the trio method; and 97, 95, and 97% with the HAP method. Accuracy of the duo method was poor (only 52% for animals genotyped with 3 K and 65% with 50K) because additional information from the paternal genotype is not used. Accuracy of the trio method was 97% with 50K but only 78% with 3K because the missing SNP were not imputed. Accuracy of the HAP method was 94% with 3 K genotypes, 98% with 50K, and 92% with nongenotyped, imputed dams. When the HAP method was extended to great-grandsires, the accuracy of maternal great-grandsire discovery was 92% for 652 Holsteins, 95% for 33 Jerseys, and 85% for 20 Brown Swiss. Accuracy was even higher using simulated genotypes. Because most dairy bulls over several generations have been genotyped, percentages of haplotypes shared with candidate males can accurately confirm, correct, or discover the sires, MGS, and even more distant ancestors of most animals.
选择、交配和改良奶牛需要准确的系谱。基因组工具允许很容易确认或发现父系祖先，因为大多数公牛都被基因分型为许多标记，但母系祖先更难发现，因为大多数母系祖先没有被基因分型。开发了三种发现母系曾祖父（MGS）的方法并进行了比较。一次计算一个单核苷酸多态性（SNP），将动物和潜在 MGS 的基因型之间的冲突（双方法）或也使用父本的基因型（三方法）。或者，通过使用跨基因座的连锁来匹配潜在 MGS 的单体型（HAP 方法），获得动物的母系单体型。双方法和三方法可以在收到基因型后立即进行，因为不需要推断。HAP 方法提高了准确性，因为使用 2683 个（3K）SNP 的基因型被推断为用于基因组评估的 45187 个（50K）SNP。使用修改后的系谱测试了 HAP 方法，其中 5%的真实 MGS 被同一年出生的随机基因分型公牛取代，5%的 MGS 设定为缺失，用于 4134 头荷斯坦牛、552 头泽西牛和 142 头棕色瑞士牛，这些牛有确认的、基因分型的公牛。对相同的动物进行了双方法和三方法的测试，只是一些动物有多个基因型，排除了推断的母畜。准确性衡量了从 12152 头荷斯坦牛、2265 头泽西牛和 1605 头棕色瑞士牛的 12152 个潜在 MGS 中选择正确的 MGS 的频率。双方法的准确性分别为 61%、60%和 65%；三方法的准确性为 95%、91%和 94%；HAP 方法的准确性为 97%、95%和 97%。双方法的准确性较差（仅 3K 基因分型动物的准确性为 52%，50K 的准确性为 65%），因为没有使用来自父本基因型的额外信息。三方法的准确性为 97%（50K），但仅为 78%（3K），因为缺失的 SNP 未推断。HAP 方法的准确性为 3K 基因型的 94%、50K 的 98%和非基因分型的、推断的母畜的 92%。当 HAP 方法扩展到曾曾祖父时，652 头荷斯坦牛、33 头泽西牛和 20 头棕色瑞士牛的母系曾曾祖父发现的准确性分别为 92%、95%和 85%。使用模拟基因型甚至更高。由于几代以来大多数奶牛公牛都已被基因分型，因此候选雄性与候选雄性共享的单体型百分比可以准确确认、更正或发现大多数动物的公牛、MGS，甚至更远的祖先。
