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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 #338025
Title: Determination of quantitative trait variants by concordance via application of the a posteriori granddaughter design to the U.S. Holstein population

Author
item WELLER, JOEL - Volcani Center (ARO)
item Bickhart, Derek
item WIGGANS, GEORGE - Retired ARS Employee
item Tooker, Melvin
item O'CONNELL, JEFFREY - University Of Maryland
item JIANG, JICAI - University Of Maryland
item Vanraden, Paul

Submitted to: Journal of Dairy Science
Publication Type: Abstract Only
Publication Acceptance Date: 2/28/2017
Publication Date: 6/24/2017
Citation: Weller, J.I., Bickhart, D.M., Wiggans, G.R., Tooker, M.E., O'Connell, J.R., Jiang, J., Van Raden, P.M. 2017. Determination of quantitative trait variants by concordance via application of the a posteriori granddaughter design to the U.S. Holstein population. Journal of Dairy Science. 100(Suppl. 2):410–411(abstr. 464).

Interpretive Summary:

Technical Abstract: Experimental designs that exploit family information can provide substantial predictive power in quantitative trait variant discovery projects. Concordance between quantitative trait locus genotype as determined by the a posteriori granddaughter design and marker genotype was determined for 29 trait-by-chromosomal segment effects segregating in the US Holstein dairy cattle (Bos taurus) population with probabilities of <10^-20. Genotypes for 79 grandsires and 16,236 sons were determined by imputation for 3,148,506 polymorphisms across the entire genome; 444 Holstein bulls had complete genome sequence, including 38 of the grandsires. Complete concordance was obtained only for daughter pregnancy rate on chromosome 18 and protein percentage on chromosome 20. For each quantitative trait locus, effects of the 20 polymorphisms with the highest concordance scores for the analyzed trait were computed by stepwise regression. The effects for stature on chromosome 7, daughter pregnancy rate on chromosome 18, and protein percentage on chromosome 20 met the following three criteria: complete or nearly complete concordance, significance of the polymorphism effect after correction for all other polymorphisms, and a marker coefficient of determination that was >50% of the total multiple-regression coefficients of determination for the 20 polymorphisms with highest concordance. An intronic variant SNP on chromosome 5 at position 93,945,738 explained 7% of the variance for fat percentage and 85% of the total variance explained by the multiple-marker regression. Variants identified in this study are likely to provide improved predictive power for genomic evaluation of dairy cattle.