Impact of genotyping strategy on the accuracy of genomic prediction in simulated populations of purebred swine

Single-step genomic BLUP (ssGBLUP) has been widely used in genomic evaluation due to relatively higher prediction accuracy and simplicity of use. The prediction accuracy from ssGBLUP depends on the amount of information available concerning both genotype and phenotype. This study investigated how information on genotype and phenotype that had been acquired from previous generations influences the prediction accuracy of ssGBLUP, and thus we sought an optimal balance about genotypic and phenotypic information to achieve a cost-effective and computationally efficient genomic evaluation. We generated two genetically correlated traits (h² = 0.35 for trait A, h² = 0.10 for trait B and genetic correlation 0.20) as well as two distinct populations mimicking purebred swine. Phenotypic and genotypic information in different numbers of previous generations and different genotyping rates for each litter were set to generate different datasets. Prediction accuracy was evaluated by correlating genomic estimated breeding values with true breeding values for genotyped animals in the last generation. The results revealed a negligible impact of previous generations that lacked genotyped animals on the prediction accuracy. Phenotypic and genotypic data, including the most recent three to four generations with a genotyping rate of 40% or 50% for each litter, could lead to asymptotic maximum prediction accuracy for genotyped animals in the last generation. Single-step genomic best linear unbiased prediction yielded an optimal balance about genotypic and phenotypic information to ensure a cost-effective and computationally efficient genomic evaluation of populations of polytocous animals such as purebred pigs.