39 Impact of inclusion rates of crossbred phenotypes and genotypes in nucleus selection programs

Abstract

Abstract The aim of this study was to investigate different inclusion rates of purebred (PB) and CB phenotypes and genotypes in genetic evaluations. Assuming PB and CB traits with moderate heritabilities (h2 = 0.4), a three-way swine crossbreeding scheme was simulated, and selection was practiced for 6 generations. The goal was to increase the CB phenotype. Phenotypes, genotypes and pedigrees for three purebred breeds (each consisting of 25 males and 175 females), F1 crosses (400 females) and terminal cross progeny (2500) were simulated using AlphaSimR. The genome consisted of 18 chromosomes with 1,800 QTL and 59.4k SNP markers. Selection was performed using EBV produced by the BLUPf90 suite of programs for each phenotyping/genotyping strategy. Strategies investigated were 1) increasing the proportion of CB with genotypes, phenotypes and sire pedigree information, 2) decreasing the proportion of PB phenotypes and genotypes, and 3) altering the genetic correlation between PB and CB traits (rpc). Each strategy was replicated 15 times. Results showed that including CB performance improved the CB phenotype regardless of rpc or phenotyping/genotyping strategy. Compared to using only PB information, including 10% of possible CB animals per generation with sire pedigrees and phenotypes increased the response in CB phenotype when rpc was 0.1, 0.3, 0.5, 0.7, and 0.9 by 192, 64, 41, 25 and 21%, respectively. Including CB genotypes dramatically improved the previously mentioned increases in response. Minimal change was observed in the CB phenotype when PB phenotypes were included or removed, if CB phenotypes, genotypes and sire pedigrees were included. PB genotypes were more informative than phenotypes in enabling prediction for CB traits. In practice, the inclusion rates of CB and PB data depends upon the degree of connectedness between CB animals and PB selection candidates and the cost-benefit ratio of increased CB performance and genotyping/phenotyping costs.