Genomic selection has been adopted nationally and internationally in different livestock and plant species. However, understanding whether genomic selection has been effective or not is an essential question for both industry and academia. Once genomic evaluation started being used, estimation of breeding values with pedigree best linear unbiased prediction (BLUP) became biased because this method does not consider selection using genomic information. Hence, the effective starting point of genomic selection can be detected in two possible ways including the divergence of genetic trends and Realized Mendelian sampling (RMS) trends obtained with BLUP and single-step genomic BLUP (ssGBLUP). This study aimed to find the start date of genomic selection for a set of economically important traits in three livestock species by comparing trends obtained using BLUP and ssGBLUP. Three datasets were used for this purpose: 1) a pig dataset with 117k genotypes and 1.3M animals in pedigree, 2) an Angus cattle dataset consisted of ~842k genotypes and 11.5M animals in pedigree, and 3) a purebred broiler chicken dataset included ~154k genotypes and 1.3M birds in pedigree were used. The genetic trends for pigs diverged for the genotyped animals born in 2014 for average daily gain (ADG) and backfat (BF). In beef cattle, the trends started diverging in 2009 for weaning weight (WW) and in 2016 for postweaning gain (PWG), with little divergence for birth weight (BTW). In broiler chickens, the genetic trends estimated by ssGBLUP and BLUP diverged at breeding cycle 6 for two out of the three production traits. The RMS trends for the genotyped pigs diverged for animals born in 2014, more for ADG than for BF. In beef cattle, the RMS trends started diverging in 2009 for WW and in 2016 for PWG, with a trivial trend for BTW. In broiler chickens, the RMS trends from ssGBLUP and BLUP diverged strongly for two production traits at breeding cycle 6, with a slight divergence for another trait. Divergence of the genetic trends from ssGBLUP and BLUP indicates the onset of the genomic selection. The presence of trends for RMS indicates selective genotyping, with or without the genomic selection. The onset of genomic selection and genotyping strategies agrees with industry practices across the three species. In summary, the effective start of genomic selection can be detected by the divergence between genetic and RMS trends from BLUP and ssGBLUP.

中文翻译：

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通过猪、肉牛和肉鸡的最佳线性无偏预测和单步基因组最佳线性无偏预测的不同趋势检测基因组选择的有效起点

基因组选择已在国内和国际上用于不同的牲畜和植物物种。然而，了解基因组选择是否有效是工业界和学术界的一个基本问题。一旦开始使用基因组评估，使用系谱最佳线性无偏预测 (BLUP) 估计育种值就会出现偏差，因为这种方法不考虑使用基因组信息进行选择。因此，可以通过两种可能的方式检测基因组选择的有效起点，包括遗传趋势的分歧和通过 BLUP 和单步基因组 BLUP (ssGBLUP) 获得的实现孟德尔抽样 (RMS) 趋势。本研究旨在通过比较使用 BLUP 和 ssGBLUP 获得的趋势，找出三种牲畜物种中一组经济上重要性状的基因组选择的开始日期。为此使用了三个数据集：1）猪数据集包含 117k 基因型和 130 万只家系动物，2）安格斯牛数据集由约 842k 基因型和 1150 万只家系动物组成，3）包括纯种肉鸡数据集使用了约 154k 基因型和 130 万只家系鸟类。对于 2014 年出生的基因型动物，猪的遗传趋势在平均日增重 (ADG) 和背膘 (BF) 方面存在差异。在肉牛中，2009 年断奶体重 (WW) 和 2016 年断奶后增重 (PWG) 趋势开始出现差异，出生体重 (BTW) 差异不大。在肉鸡中，ssGBLUP 和 BLUP 估计的遗传趋势在三个生产性状中的两个在育种周期 6 出现了分歧。对于 2014 年出生的动物，基因型猪的 RMS 趋势不同，ADG 比 BF 更大。在肉牛中，2009 年 WW 和 2016 年 PWG 的 RMS 趋势开始出现差异，BTW 的趋势微乎其微。在肉鸡中，ssGBLUP 和 BLUP 的 RMS 趋势在育种周期 6 的两个生产性状上差异很大，在另一个性状上略有差异。来自 ssGBLUP 和 BLUP 的遗传趋势的分歧表明基因组选择的开始。RMS 趋势的存在表明选择性基因分型，有或没有基因组选择。基因组选择和基因分型策略的开始与三个物种的行业实践一致。总之，