Abstract
BackgroundUnderstanding 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.MethodsWe 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.ResultsThe 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.ConclusionsOur 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.
Highlights
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
The breeding values predicted by pedigree-based best linear unbiased prediction (PBLUP) for these animals are, on average, underestimated [11], while single-step genomic best linear unbiased prediction (BLUP) is expected to provide unbiased genetic trends [12, 13] because it combines all the information that has been used for selection decisions
For ADG and FEED, the genetic trends estimated using PBLUP and single-step genomic BLUP (ssGBLUP) started to diverge in 2018, but for birth weight (BW), which is not under direct selection, there was no evidence of divergence
Summary
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. Genomic preselection occurs when only animals that are selected based on genomic estimated breeding values (GEBV), and on positive Mendelian sampling terms, are phenotyped [9, 10] In this case, the breeding values predicted by PBLUP for these animals are, on average, underestimated [11], while single-step genomic BLUP (ssGBLUP) is expected to provide unbiased genetic trends [12, 13] because it combines all the information that has been used for selection decisions (pedigree, genomic data, and phenotypic records). The point when estimated genetic trends based on PBLUP and ssGBLUP diverge indicates the starting date of effective genomic selection [13] This is the timepoint when young animals are selected based on estimates of their Mendelian sampling terms based on genomics, in addition to parent average and, perhaps, own information. If multiple-trait selection is practiced, it is important that the genetic trends are estimated using a multiple-trait model
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