RT Journal Article
SR Electronic
T1 Detecting effective starting point of genomic selection by divergent trends from BLUP and ssGBLUP in pigs, beef cattle, and broilers
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.05.28.446145
DO 10.1101/2021.05.28.446145
A1 Rostam Abdollahi-Arpanahi
A1 Daniela Lourenco
A1 Ignacy Misztal
YR 2021
UL http://biorxiv.org/content/early/2021/05/28/2021.05.28.446145.abstract
AB 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 BLUP became biased because this method does not consider selection using genomic information. Hence, the effective start 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. For this purpose, three datasets comprised a pig dataset with 117k genotypes and 1.3M animals in pedigree, Angus cattle dataset consisted of ~842k genotypes and 11.5M animals in pedigree, and 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 and backfat. In beef cattle, the trends started diverging in 2009 for weaning weight and in 2016 for postweaning gain, with little diverging for birth weight. In broiler chickens, the genetic trends estimated by ssGBLUP and BLUP diverged at breeding cycle 6 for two out of three production traits. The RMS trends for the genotyped pigs diverged for animals born in 2014, more for average daily gain than for backfat. In beef cattle, the RMS trends started diverging in 2009 for weaning weight and in 2016 for postweaning gain, with a trivial trend for birth weight. 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 onset of the genomic selection. Presence of trends for RMS indicates selective genotyping, with or without the genomic selection. The onset of genomic selection and genotyping strategies agree with industry practices across the 3 species. In summary, the effective start of genomic selection can be detected by the divergence between genetic and RMS trends from BLUP and ssGBLUP.Competing Interest StatementThe authors have declared no competing interest.List of AbbreviationsBLUPBest Linear Unbiased PredictionssGBLUPsingle step Genomic Best Linear Unbiased PredictionEBVEstimated Breeding Value(s)GEBVGenomic Estimated Breeding Value(s)SNPSingle Nucleotide PolymorphismRMSRealized Mendelian SamplingAPYAlgorithm for Proven and YoungADGAverage Daily GainBFBackfatBTWBirth WeightWWWeaning WeightPWGPost Weaning GainPAParent AveragePCProgeny ContributionYDYield DeviationGIGenomic Information