Selective genotyping and phenotypic data inclusion strategies of crossbred progeny for combined crossbred and purebred selection in swine breeding

Inclusion of crossbred (CB) data into traditionally purebred (PB) genetic evaluations has been shown to increase the response in CB performance. Currently, it is unrealistic to collect data on all CB animals in swine production systems, thus, a subset of CB animals must be selected to contribute genomic/phenotypic information. The aim of this study was to evaluate selective genotyping strategies in a simulated 3-way swine crossbreeding scheme. The swine crossbreeding scheme was simulated and produced 3-way CB animals for 6 generations with 3 distinct PB breeds each with 25 and 175 mating males and females, respectively. F1 crosses (400 mating females) produced 4,000 terminal CB progeny which were subjected to selective genotyping. The genome consisted of 18 chromosomes with 1,800 QTL and 72k SNP markers. Selection was performed using estimated breeding values (EBV) for CB performance. It was assumed that both PB and CB performance was moderately heritable (h2=0.4). Several scenarios altering the genetic correlation between PB and CB performance (rpc=0.1, 0.3, 0.5, 0.7,or 0.9) were considered. CB animals were chosen based on phenotypes to select 200, 400, or 800 CB animals to genotype per generation. Selection strategies included: (1) Random: random selection, (2) Top: highest phenotype, (3) Bottom: lowest phenotype, (4) Extreme: half highest and half lowest phenotypes, and (5) Middle: average phenotype. Each selective genotyping strategy, except for Random, was considered by selecting animals in half-sib (HS) or full-sib (FS) families. The number of PB animals with genotypes and phenotypes each generation was fixed at 1,680. Each unique genotyping strategy and rpc scenario was replicated 10 times. Selection of CB animals based on the Extreme strategy resulted in the highest (P < 0.05) rates of genetic gain in CB performance (ΔG) when rpc<0.9. For highly correlated traits (rpc=0.9) selective genotyping did not impact (P > 0.05) ΔG. No differences (P > 0.05) were observed in ΔG between top, bottom, or middle when rpc>0.1. Higher correlations between true breeding values (TBV) and EBV were observed using Extreme when rpc<0.9. In general, family sampling method did not impact ΔG or the correlation between TBV and EBV. Overall, the Extreme genotyping strategy produced the greatest genetic gain and the highest correlations between TBV and EBV, suggesting that 2-tailed sampling of CB animals is the most informative when CB performance is the selection goal.