In this study, we conducted genomic prediction for two Yorkshire purebred populations (Yichun and Chifeng) from two different provinces of China that both had a limited population size. Two growth traits (age adjusted to 100 kg weight, AGE; back‐fat thickness adjusted to 100 kg weight, BF) and one reproduction trait (total number of piglets born, TNB) were analyzed with four prediction strategies: one‐population BLUP, joint two‐population BLUP, one‐population single‐step BLUP (SSBLUP) and joint two‐population SSBLUP. Our results illustrate that accuracies of genomic estimated breeding values were improved for BF and TNB for the Yichun population and for BF for the Chifeng population by genomic prediction (one‐population SSBLUP and joint two‐population SSBLUP). The accuracy of TNB for the Yichun population was increased two fold when comparing the one‐population SSBLUP to the one‐population BLUP prediction. Meanwhile, prediction biases were dramatically reduced for AGE for the Yichun population and for TNB for the Chifeng population. The conclusions of this study are as follows: first, genomic prediction is useful for improving prediction accuracy for purebred pig breeding farms with a limited population size; second, joint genomic prediction for different populations of the same breed with certain genetic links has the trend to further improve prediction accuracy.

Self-developed swine 55K SNP chip-V1Information about self-developed swine 55K SNP chip, including marker names, chromosomes, positions, sequences, et al.Self-developed swine 50k SNP chip-V2SNP marker information for self-developed chip V2, including markers' name, chromosomes and positionsOverlap SNPs between V1 and V2 panelsInformation about overlaped SNPs between V1 and V2 panels