Genomic predictions for yield traits in US Holsteins with unknown parent groups

Abstract

The objective of this study was to assess the reliability and bias of estimated breeding values (EBV) from traditional BLUP with unknown parent groups (UPG), genomic EBV (GEBV) from single-step genomic BLUP (ssGBLUP) with UPG for the pedigree relationship matrix (A) only (SS_UPG), and GEBV from ssGBLUP with UPG for both A and the relationship matrix among genotyped animals (A22; SS_UPG2) using 6 large phenotype-pedigree truncated Holstein data sets. The complete data included 80 million records for milk, fat, and protein yields from 31 million cows recorded since 1980. Phenotype-pedigree truncation scenarios included truncation of phenotypes for cows recorded before 1990 and 2000 combined with truncation of pedigree information after 2 or 3 ancestral generations. A total of 861,525 genotyped bulls with progeny and cows with phenotypic records were used in the analyses. Reliability and bias (inflation/deflation) of GEBV were obtained for 2,710 bulls based on deregressed proofs, and on 381,779 cows born after 2014 based on predictivity (adjusted cow phenotypes). The BLUP reliabilities for young bulls varied from 0.29 to 0.30 across traits and were unaffected by data truncation and number of generations in the pedigree. Reliabilities ranged from 0.54 to 0.69 for SS_UPG and were slightly affected by phenotype-pedigree truncation. Reliabilities ranged from 0.69 to 0.73 for SS_UPG2 and were unaffected by phenotype-pedigree truncation. The regression coefficient of bull deregressed proofs on (G)EBV (i.e., GEBV and EBV) ranged from 0.86 to 0.90 for BLUP, from 0.77 to 0.94 for SS_UPG, and was 1.00 ± 0.03 for SS_UPG2. Cow predictivity ranged from 0.22 to 0.28 for BLUP, 0.48 to 0.51 for SS_UPG, and 0.51 to 0.54 for SS_UPG2. The highest cow predictivities for BLUP were obtained with the most extreme truncation, whereas for SS_UPG2, cow predictivities were also unaffected by phenotype-pedigree truncations. The regression coefficient of cow predictivities on (G)EBV was 1.02 ± 0.02 for SS_UPG2 with the most extreme truncation, which indicated the least biased predictions. Computations with the complete data set took 17 h with BLUP, 58 h with SS_UPG, and 23 h with SS_UPG2. The same computations with the most extreme phenotype-pedigree truncation took 7, 36, and 15 h, respectively. The SS_UPG2 converged in fewer rounds than BLUP, whereas SS_UPG took up to twice as many rounds. Thus, the ssGBLUP with UPG assigned to both A and A22 provided accurate and unbiased evaluations, regardless of phenotype-pedigree truncation scenario. Old phenotypes (before 2000 in this data set) did not affect the reliability of predictions for young selection candidates, especially in SS_UPG2.