Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA.
J Anim Sci. 2021 Sep 1;99(9). doi: 10.1093/jas/skab243.
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.
基因组选择已在不同的家畜和植物物种中在国内外得到采用。然而，了解基因组选择是否有效是行业和学术界的一个重要问题。一旦开始使用基因组评估，使用系谱最佳线性无偏预测（BLUP）估计育种值就会产生偏差，因为该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法检测到基因组选择的有效起始点，包括使用 BLUP 和单步基因组最佳线性无偏预测（ssGBLUP）获得的遗传趋势和实现的孟德尔抽样（RMS）趋势的差异。本研究旨在通过比较使用 BLUP 和 ssGBLUP 获得的趋势，找到三个家畜物种中一组经济重要性状的基因组选择开始日期。为此，使用了三个数据集：1）一个具有 117k 个基因型和 1300 万只动物的猪数据集，2）一个由842k 个基因型和 1150 万只动物组成的安格斯牛数据集，3）一个包括154k 个基因型和 130 万只鸟类的纯系肉鸡数据集。对于平均日增重（ADG）和背膘（BF），2014 年出生的基因分型动物的遗传趋势开始出现分歧。在肉牛中，2009 年断奶体重（WW）和 2016 年断奶后增重（PWG）的趋势开始出现分歧，出生体重（BTW）的分歧很小。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性状的 6 个繁殖周期中出现分歧。对于 2014 年出生的动物，RMS 趋势对于 ADG 的分歧大于 BF。在肉牛中，2009 年 WW 和 2016 年 PWG 的 RMS 趋势开始出现分歧，BTW 的趋势微不足道。在肉鸡中，ssGBLUP 和 BLUP 的 RMS 趋势在繁殖周期 6 时强烈分歧，另一个性状略有分歧。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，无论是否存在基因组选择。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，可以通过 BLUP 和 ssGBLUP 的遗传和 RMS 趋势之间的差异来检测基因组选择的有效开始。
