![]() ![]() The Philippine Carabao Center (PCC) has put in place a genetic improvement program that includes a system of evaluating genetically superior individual animals for milk and milk component traits and maintenance of nucleus herds of dairy buffaloes as source of breeding animals and provision of frozen semen from the best riverine buffalo germplasm (identified through progeny testing) for artificial insemination (AI). Average GBLUP and ssGBLUP slopes were 0.89 and 0.84, respectively, whereas the average pBLUP (for GENO and ALL data) slopes were 0.80 and 0.54, respectively. Slopes of the two genomic methods were also closer to one, indicating lesser bias, compared to pBLUP. Average GBLUP and ssGBLUP accuracies were 0.24 and 0.29, respectively, whereas average pBLUP accuracies (for GENO and ALL data) were 0.21 and 0.22, respectively. Results showed that genomic methods (GBLUP and ssGBLUP) provide more accurate predictions compared to pBLUP. To assess the bias of the prediction, the regression coefficient (slope) of the adjusted phenotypes on the predicted BVs was also calculated. Accuracy of prediction was calculated as the correlation between the predicted BVs of the test set and adjusted phenotypes, which were corrected for fixed effects, divided by the square root of the heritability of the trait, corrected for the number of lactations used in the test set. A pedigree file containing 2,642 animals was used for pBLUP and ssGBLUP. After quality control, 60,827 single-nucleotide polymorphisms were used for downward analysis. Animals were genotyped with the Affymetrix 90k buffalo genotyping array. ![]() The ALL data, consisting of the GENO data plus females with phenotypes but not genotyped ( n = 1,975 with 3,821,305-days lactation records), were analyzed using pBLUP and ssGBLUP. The GENO data consisting of all female buffaloes that have both phenotypes and genotypes ( n = 904 with 1,773,305-days lactation records) were analyzed using pBLUP and GBLUP. To also assess the bias of the prediction, the regression coefficient (slope) of the adjusted phenotypes on the predicted breeding values (BVs) was also calculated. The objective of this study was to compare the accuracies of genomic prediction for milk yield, fat yield, and protein yield from Philippine dairy buffaloes using genomic best linear unbiased prediction (GBLUP) and single-step GBLUP (ssGBLUP) with the accuracies based on pedigree BLUP (pBLUP). ![]() 3Philippine Carabao Center National Headquarters, Muñoz, Philippines.2Philippine Carabao Center- University of the Philippines Los Banos, Laguna, Philippines.1School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia. ![]() Flores 3, Naomi Duijvesteijn 1*, Nasir Moghaddar 1 and Julius H. ![]()
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