The accuracy of breeding values for body size latent trait in pigs under different prediction models

The present study was performed to quantify a latent variable for body size (BS) from the five linear body measurements, including body length (BL), body height (BH), chest width (CW), chest girth (CG), and tube girth (TG). The study population consisted of N= 5573 Yorkshire pigs, 592 individuals out of them were genotyped using a PorcineSNP80 BeadChip. The body size latent variable was determined using Confirmatory Factor Analysis (CFA). Then, the accuracy of breeding values was obtained using pedigree-based best linear unbiased prediction (PBLUP), genomic best linear unbiased prediction (GBLUP), and single-step genomic best linear unbiased prediction (ssGBLUP) models. The overall fit indices, including standardized root mean square residual (SRMR), root mean square error of approximation (RMSEA), Tucker-Lewis Index (TLI), and comparative fit index (CFI) were obtained for the BS as 0.03, 0.09, 0.93, and 0.96, respectively which imply the adequacy of the considered model for BS construct. The performance of models was measured in a 5-fold cross-validation with 10 repeats to get a more accurate measure of the model's performance. The accuracy of models was compared via the correlation between predicted breeding values (PBV) and estimated breeding values (EBV) metric which was 0.37, 0.30, and 0.28 for PBLUP, ssGBLUP, and GBLUP, respectively. Furthermore, the goodness of fit is measured by the mean square of error (MSE) and Pearson's correlations r(y, ) between observed and predicted phenotypes. The lowest MSE and the highest Pearson's correlations were obtained under PBLUP while the highest MSE and the lowest Pearson's correlations were obtained under GBLUP. The obtained results showed the GBLUP method generally provided lower prediction accuracies than PBLUP and ssGBLUP methods, and also ssGBLUP generated lower prediction accuracy than traditional PBLUP. The performance of ssGBLUP and GBLUP was lower than expected mainly due to the small number of genotyped animals.