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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 #342125
Title: Differing genetic trend estimates from traditional and genomic evaluations for genotyped animals as evidence of pre-selection bias in US Holsteins

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

Submitted to: Journal of Dairy Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/10/2017
Publication Date: 6/1/2018
Citation: Masuda, Y., Van Raden, P.M., Misztal, I., Lawlor, T.J. 2018. Differing genetic trend estimates from traditional and genomic evaluations for genotyped animals as evidence of pre-selection bias in US Holsteins. Journal of Dairy Science. 101(6):5194–5206. https://doi.org/10.3168/jds.2017-13310.
DOI: https://doi.org/10.3168/jds.2017-13310

Interpretive Summary: Production traits of over 20 million US Holsteins were analyzed by BLUP and single-step GBLUP (ssGBLUP) using genotypes on over 760,000 animals. ssGBLUP analyzes genotypes, pedigrees and genotypes jointly. For genotyped cows born after 2006, the genetic trend leveled off with BLUP but was similar with single-step GBLUP. For genotyped bulls born after 2008, the trend was lower with BLUP but with smaller differences than in cows. BLUP seems affected by genomic pre-selection bias while ssGBLUP seems to account for it.

Technical Abstract: The objective of this study was to compare genetic trends from a single-step genomic BLUP (ssGBLUP) and the traditional BLUP models for milk production traits in US Holstein. 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. Genotypes for 764,029 animals were utilized, and analyzes were by a three-trait repeatability model as 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 BLUP) 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 BLUP took 6.5 hours and 1.4 GB of memory, and computations with ssGBLUP took 13 hours and 115 GB of memory. For genotyped sires with at least 10 daughters, the trends for PTA and GPTA were similar up to 2008, with a higher trend for ssGBLUP later (approximately by 36 kg milk, 2.1 kg fat and 1.1 kg protein for bulls born in 2010). For genotyped cows, the trends were similar up to 2006, with a higher trend for ssGBLUP later (approximately by 91 kg milk, 3.6 kg fat and 2.7 kg protein for cows born in 2012). For all cows, the trends were slightly higher for ssGBLUP, with much smaller differences than for genotyped cows. Trends for BLUP indicate bias due to genomic pre-selection for genotyped sires and cows. The single-step genomic BLUP seems to at least partially account for that bias and is computationally suitable for national evaluations.