Abstract
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). 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. Two data sets were analyzed. 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. 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. Animals were genotyped with the Affymetrix 90k buffalo genotyping array. After quality control, 60,827 single-nucleotide polymorphisms were used for downward analysis. A pedigree file containing 2,642 animals was used for pBLUP and ssGBLUP. 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. To assess the bias of the prediction, the regression coefficient (slope) of the adjusted phenotypes on the predicted BVs was also calculated. Results showed that genomic methods (GBLUP and ssGBLUP) provide more accurate predictions 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. Slopes of the two genomic methods were also closer to one, indicating lesser bias, compared to pBLUP. 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.
Highlights
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 for artificial insemination (AI)
The objective of this study was to determine the accuracy of genomic prediction and bias for milk yield (MY), fat yield (FY), and protein yield (PY) from Philippine dairy buffaloes using genomic best linear unbiased prediction (GBLUP) and single-step GBLUP (ssGBLUP) compared to prediction accuracy and bias based on pedigree BLUP
Results showed that genomic methods (GBLUP and ssGBLUP) provide more accurate predictions compared to pedigree BLUP (pBLUP)
Summary
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). PCC maintains 12 institutional herds of dairy buffaloes [mostly Bulgarian Murrahs (BUL)] dispersed throughout the archipelago as source of breeding animals and frozen semen from the best riverine buffalo germplasm for AI to riverine, crossbred, and swamp buffaloes. When the trait of interest cannot be recorded on the selection candidate, genomic selection schemes are very attractive even when the number of phenotypic records is limited, because traditional breeding requires progeny testing schemes with long generation intervals (Schaeffer, 2006). Having similarities with dairy cattle breeding, for example, long generation interval, traits that are sex-limited, and measured late in life, it is probable that the advantages of genomic selection seen in dairy cattle will be observed in dairy buffalo
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