Understanding whether genomic selection has been effective in livestock and when the results of genomic selection became visible are essential questions which we have addressed in this paper. Three criteria were used to identify practices of breeding programs over time: (1) the point of divergence of estimated genetic trends based on pedigree-based best linear unbiased prediction (BLUP) versus single-step genomic BLUP (ssGBLUP), (2) the point of divergence of realized Mendelian sampling (RMS) trends based on BLUP and ssGBLUP, and (3) the partition of genetic trends into that contributed by genotyped and non-genotyped individuals and by males and females. We used data on 282,035 animals from a commercial maternal line of pigs, of which 32,856 were genotyped for 36,612 single nucleotide polymorphisms (SNPs) after quality control. Phenotypic data included 228,427, 101,225, and 11,444 records for birth weight, average daily gain in the nursery, and feed intake, respectively. Breeding values were predicted in a multiple-trait framework using BLUP and ssGBLUP. The points of divergence of the genetic and RMS trends estimated by BLUP and ssGBLUP indicated that genomic selection effectively started in 2019. Partitioning the overall genetic trends into that for genotyped and non-genotyped individuals revealed that the contribution of genotyped animals to the overall genetic trend increased rapidly from ~ 74% in 2016 to 90% in 2019. The contribution of the female pathway to the genetic trend also increased since genomic selection was implemented in this pig population, which reflects the changes in the genotyping strategy in recent years. Our results show that an assessment of breeding program practices can be done based on the point of divergence of genetic and RMS trends between BLUP and ssGBLUP and based on the partitioning of the genetic trend into contributions from different selection pathways. However, it should be noted that genetic trends can diverge before the onset of genomic selection if superior animals are genotyped retroactively. For the pig population example, the results showed that genomic selection was effective in this population.

中文翻译：

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剖析遗传趋势以了解家畜育​​种实践：母猪系示例

了解基因组选择对家畜是否有效以及基因组选择的结果何时可见是我们在本文中解决的基本问题。三个标准用于确定育种计划随时间的实践：（1）基于谱系的最佳线性无偏预测（BLUP）与单步基因组BLUP（ssGBLUP）的估计遗传趋势的分歧点，（2）基于 BLUP 和 ssGBLUP 的已实现的孟德尔采样 (RMS) 趋势的分歧点，以及 (3) 将遗传趋势划分为由基因分型和非基因分型个体以及男性和女性贡献的趋势。我们使用了来自商业母猪品系的 282,035 只动物的数据，其中 32,856 只在质量控制后进行了 36,612 个单核苷酸多态性 (SNP) 的基因分型。表型数据分别包括 228,427、101,225 和 11,444 条出生体重、托儿所平均日增重和采食量记录。使用 BLUP 和 ssGBLUP 在多性状框架中预测育种值。BLUP 和 ssGBLUP 估计的遗传和 RMS 趋势的分歧点表明基因组选择在 2019 年有效开始。从 2016 年的约 74% 迅速增加到 2019 年的 90%。 自从在该猪群中实施基因组选择以来，雌性途径对遗传趋势的贡献也有所增加，这反映了近年来基因分型策略的变化。我们的结果表明，可以根据 BLUP 和 ssGBLUP 之间的遗传和 RMS 趋势的分歧点以及根据将遗传趋势划分为来自不同选择途径的贡献来评估育种计划实践。然而，应该注意的是，如果对优良动物进行追溯基因分型，则在基因组选择开始之前，遗传趋势可能会发生分歧。对于猪群的例子，结果表明基因组选择在这个群体中是有效的。应该注意的是，如果对优良动物进行追溯基因分型，则在基因组选择开始之前，遗传趋势可能会发生分歧。对于猪群的例子，结果表明基因组选择在这个群体中是有效的。应该注意的是，如果对优良动物进行追溯基因分型，则在基因组选择开始之前，遗传趋势可能会发生分歧。对于猪群的例子，结果表明基因组选择在这个群体中是有效的。