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Use of Genomic Recursions and Algorithm for Proven and Young Animals for Single-Step Genomic BLUP Analyses with a Large Number of Genotypes
The purpose of this study was to evaluate accuracy of genomic selection in single-step genomic BLUP (ssGBLUP) when the inverse of the genomic relationship matrix (G) is derived by the algorithm for proven and young animals (APY). This algorithm implements the inversion of G by genomic recursions. With efficient implementation, the algorithm has a cubic cost for proven animals but only a linear cost for young animals. Analyses involved simulated genomic data consisting of 20k genotyped animals for 45k SNP and real final score data for 74,980 genotyped Holstein bulls. The correlation between APY and regular genomic EBV of genotyped animals was >0.96 for simulated data under selection. For the real data, the correlation was >0.99. The APY algorithm may allow using all the available genotypes in one ssGBLUP analysis to reduce biases due to preselection of young animals.
Keywords:
single-step method
genomic selection
