Comparison of the Efficiency of BLUP and GBLUP in Genomic Prediction of Immune Traits in Chickens

Simple Summary With the rapid development of the poultry industry, outbreaks of certain avian diseases such as avian influenza, Newcastle disease, and salmonellosis can cause severe loss to local economies. An effective method to avoid this problem may be developing resistant lines on the basis of immune response traits. In our study, when the number of genotyped reference animals was small, the traditional pedigree-based method (BLUP) was more efficient than the genetic linear unbiased prediction of genomes (GBLUP) method in predicting the genetic parameters of sheep red blood cell antibody titer (SRBC), the ratio of heterophils to lymphocytes (H/L), the spleen immune index (SII) and the spleen weight at 100 d (SW) in Beijing oil chickens. Abstract Poultry diseases pose a large threat to poultry production. Selection to improve immune traits is a feasible way to prevent and control avian diseases. The objective of this study was to investigate the efficiency of estimation of genetic parameters for antibody response to avian influenza virus (Ab-AIV), antibody response to Newcastle disease virus (Ab-NDV), sheep red blood cell antibody titer (SRBC), the ratio of heterophils to lymphocytes (H/L), immunoglobulin G (IgG), the spleen immune index (SII), thymus immune index (TII), thymus weight at 100 d (TW) and the spleen weight at 100 d (SW) in Beijing oil chickens, by using the best linear unbiased prediction (BLUP) method and genomic best linear unbiased prediction (GBLUP) method. The phenotypic data used in the two methods were the same and were from 519 individuals. With the BLUP model, Ab-AIV, Ab-NDV, SRBC, H/L, IgG, TII, and TW had low heritability ranging from 0.000 to 0.281, whereas SII and SW had high heritability of 0.631 and 0.573. With the GBLUP model, all individuals were genotyped with Illumina 60K SNP chips, and Ab-AIV, Ab-NDV, SRBC, H/L and IgG had low heritability ranging from 0.000 to 0.266, whereas SII, TII, TW and SW had moderate heritability ranging from 0.300 to 0.472. We compared the prediction accuracy obtained from BLUP and GBLUP through 50 time 5-fold cross-validation (CV), and the results indicated that BLUP provided a slightly higher accuracy of prediction than GBLUP in this population.