Using pooled data for genomic prediction in a bivariate framework with missing data.

Pooling samples to derive group genotypes can enable the economically efficient use of commercial animals within genetic evaluations. To test a multivariate framework for genetic evaluations using pooled data, simulation was used to mimic a beef cattle population including two moderately heritable traits with varying genetic correlations, genotypes and pedigree data. There were 15 generations (n = 32,000; random selection and mating), and the last generation was subjected to genotyping through pooling. Missing records were induced in two ways: (a) sequential culling and (b) random missing records. Gaps in genotyping were also explored whereby genotyping occurred through generation 13 or 14. Pools of 1, 20, 50 and 100 animals were constructed randomly or by minimizing phenotypic variation. The EBV was estimated using a bivariate single-step genomic best linear unbiased prediction model. Pools of 20 animals constructed by minimizing phenotypic variation generally led to accuracies that were not different than using individual progeny data. Gaps in genotyping led to significantly different EBV accuracies (p < .05) for sires and dams born in the generation nearest the pools. Pooling of any size generally led to larger accuracies than no information from generation 15 regardless of the way missing records arose, the percentage of records available or the genetic correlation. Pooling to aid in the use of commercial data in genetic evaluations can be utilized in multivariate cases with varying relationships between the traits and in the presence of systematic and randomly missing phenotypes.

Genomic prediction using pooled data in a single-step genomic best linear unbiased prediction framework.

Economically relevant traits are routinely collected within the commercial segments of the beef industry but are rarely included in genetic evaluations because of unknown pedigrees. Individual relationships could be resurrected with genomics, but this would be costly; therefore, pooling DNA and phenotypic data provide a cost-effective solution. Pedigree, phenotypic, and genomic data were simulated for a beef cattle population consisting of 15 generations. Genotypes mimicked a 50k marker panel (841 quantitative trait loci were located across the genome, approximately once per 3 Mb) and the phenotype was moderately heritable. Individuals from generation 15 were included in pools (observed genotype and phenotype were mean values of a group). Estimated breeding values (EBV) were generated from a single-step genomic best linear unbiased prediction model. The effects of pooling strategy (random and minimizing or uniformly maximizing phenotypic variation within pools), pool size (1, 2, 10, 20, 50, 100, or no data from generation 15), and generational gaps of genotyping on EBV accuracy (correlation of EBV with true breeding values) were quantified. Greatest EBV accuracies of sires and dams were observed when there was no gap between genotyped parents and pooled offspring. The EBV accuracies resulting from pools were usually greater than no data from generation 15 regardless of sire or dam genotyping. Minimizing phenotypic variation increased EBV accuracy by 8% and 9% over random pooling and uniformly maximizing phenotypic variation, respectively. A pool size of 2 was the only scenario that did not significantly decrease EBV accuracy compared with individual data when pools were formed randomly or by uniformly maximizing phenotypic variation (P > 0.05). Pool sizes of 2, 10, 20, or 50 did not generally lead to statistical differences in EBV accuracy than individual data when pools were constructed to minimize phenotypic variation (P > 0.05). Largest numerical increases in EBV accuracy resulting from pooling compared with no data from generation 15 were seen with sires with prior low EBV accuracy (those born in generation 14). Pooling of any size led to larger EBV accuracies of the pools than individual data when minimizing phenotypic variation. Resulting EBV for the pools could be used to inform management decisions of those pools. Pooled genotyping to garner commercial-level phenotypes for genetic evaluations seems plausible although differences exist depending on pool size and pool formation strategy.

The impact of clustering methods for cross-validation, choice of phenotypes, and genotyping strategies on the accuracy of genomic predictions.

For genomic predictors to be of use in genetic evaluation, their predicted accuracy must be a reliable indicator of their utility, and thus unbiased. The objective of this paper was to evaluate the accuracy of prediction of genomic breeding values (GBV) using different clustering strategies and response variables. Red Angus genotypes (n = 9,763) were imputed to a reference 50K panel. The influence of clustering method [k-means, k-medoids, principal component (PC) analysis on the numerator relationship matrix (A) and the identical-by-state genomic relationship matrix (G) as both data and covariance matrices, and random] and response variables [deregressed estimated breeding values (DEBV) and adjusted phenotypes] were evaluated for cross-validation. The GBV were estimated using a Bayes C model for all traits. Traits for DEBV included birth weight (BWT), marbling (MARB), rib-eye area (REA), and yearling weight (YWT). Adjusted phenotypes included BWT, YWT, and ultrasonically measured intramuscular fat percentage and REA. Prediction accuracies were estimated using the genetic correlation between GBV and associated response variable using a bivariate animal model. A simulation mimicking a cattle population, replicated 5 times, was conducted to quantify differences between true and estimated accuracies. The simulation used the same clustering methods and response variables, with the addition of 2 genotyping strategies (random and top 25% of individuals), and forward validation. The prediction accuracies were estimated similarly, and true accuracies were estimated as the correlation between the residuals of a bivariate model including true breeding value (TBV) and GBV. Using the adjusted Rand index, random clusters were clearly different from relationship-based clustering methods. In both real and simulated data, random clustering consistently led to the largest estimates of accuracy, while no method was consistently associated with more or less bias than other methods. In simulation, random genotyping led to higher estimated accuracies than selection of the top 25% of individuals. Interestingly, random genotyping seemed to overpredict true accuracy while selective genotyping tended to underpredict accuracy. When forward in time validation was used, DEBV led to less biased estimates of GBV accuracy. Results suggest the highest, least biased GBV accuracies are associated with random genotyping and DEBV.