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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #338674
Title: Genetic trends from single-step GBLUP and traditional BLUP for production traits in US Holstein

Author
item MASUDA, YATAKA - University Of Georgia
item MISZTAL, IGNACY - University Of Georgia
item Vanraden, Paul
item LAWLOR, TOM - Holstein Association Usa, Inc

Submitted to: Journal of Dairy Science
Publication Type: Abstract Only
Publication Acceptance Date: 3/15/2017
Publication Date: 6/24/2017
Citation: Masuda, Y., Misztal, I., Van Raden, P.M., Lawlor, T. 2017. Genetic trends from single-step GBLUP and traditional BLUP for production traits in US Holstein. Journal of Dairy Science. 100(Suppl. 2):410(abstr. 462).

Interpretive Summary:

Technical Abstract: The objective of this study was to compare genetic trends from a single-step genomic BLUP (ssGBLUP) and the traditional BLUP (tradBLUP) models for milk production traits in US Holstein. We used 764,029 genotyped animals in this study. Phenotypes were 305-day milk, fat, and protein yield from 21,527,040 cows recorded between January, 1990 and August, 2015. The pedigree file included 29,651,623 animals limited to 3 generations back from recorded or genotyped animals. We applied a three-trait repeatability model with the same genetic parameters used in the US official genetic evaluation. Unknown parent groups were incorporated into the inverse of a relationship matrix (H^-1 in ssGBLUP and A^-1 in tradBLUP) with the QP-transformation. In ssGBLUP, 18,359 genotyped animals were randomly chosen as core animals to calculate the inverse of genomic relationship matrix with the APY algorithm. Computations with tradBLUP took 6.5 hours and 1.4 GB of memory, and computations with ssGBLUP took 13 hours and 115 GB of memory. Estimated breeding values were adjusted to a genetic base on recorded cows born in 2000 in each model and converted to GPTA in ssGBLUP and PTA in tradBLUP. For genotyped sires with at least 50 daughters with phenotype(s) born between 2000 and 2010, the genetic trend of GPTA was always greater than PTA in all traits. The difference in two genetic trends was almost constant for the sires born up to 2008 (on average, 11 kg in milk, 0.5 kg in fat, and 0.3 kg in protein yield) and the difference was greater in the last 2 years. The difference between the GPTA means for the bulls born in 2010 was 35 kg for milk, 2.2 kg for fat, and 1.2 kg for protein yield. For genotyped cows with phenotype(s), the GPTA trend was identical to or slightly greater than the PTA trend up to 2006. Two trends started to diverge obviously in 2007 and the GPTA trend kept rising while the PTA trend remained at the same level. The single-step method provides very similar genetic trends to the traditional evaluations except for the last few years. The recent lower PTA trend can be due to a downward bias caused with genomic pre-selection of young animals.