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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 #335601

Title: Determination of quantitative trait nucleotides by concordance analysis between quantitative trait loci and marker genotypes of US Holsteins

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 RON, M - Volcani Center (ARO)
item Vanraden, Paul

Submitted to: Journal of Dairy Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/19/2018
Publication Date: 7/18/2018
Citation: Weller, J.I., Bickhart, D.M., Wiggans, G.R., Tooker, M.E., O'Connell, J.R., Jiang, J., Ron, M., Van Raden, P.M. 2018. Determination of quantitative trait nucleotides by concordance analysis between quantitative trait loci and marker genotypes of US Holsteins. Journal of Dairy Science. 101(10):9089–9107.

Interpretive Summary: Identification of natural genetic mutations that may alter livestock animal production is an important pursuit, as it is far more reliable to estimate the effects these variants have on the animal if they are tracked directly. Unfortunately, these variants are difficult to accurately predict as our knowledge of the complex biological systems of livestock is still in its infancy. Here, we demonstrate that a method that uses an improved experimental design is able to identify these variants (or those in extremely close proximity) and may thereby improve genetic marker tools in the future.

Technical Abstract: Experimental design that exploits family information can provide substantial predictive power in variant discovery projects. Concordance between quantitative trait loci (QTL) genotype, as determined by the a posteriori granddaughter design and marker genotype was determined for 29 QTL segregating in the US Holstein dairy cattle (Bos taurus) population with probabilities < 10^-20. Genotypes for 79 grandsires and 16,236 sons were determined by imputation for 3,148,506 polymorphisms spanning the entire genome, based on 444 Holstein bulls with complete genome sequence, including 38 of the grandsires. Complete concordance was obtained only for daughter pregnancy rate on chromosome 18 and protein % on chromosome 20. A missense mutation in the growth hormone reception gene described previously in the Dutch Holstein population displayed complete concordance for the latter effect. For each QTL the effects of the 20 polymorphisms with the highest concordance scores on the trait analyzed were computed by stepwise regression. The effects of stature on chromosome 7, daughter pregnancy rate on chromosome 18, and protein % on chromosome 20 met the following three criteria: complete or nearly complete concordance, significance of the effect of polymorphism after correction for all other polymorphisms, and R^2 for the marker was > 50% of the total multiple regression R^2 including the 20 polymorphisms. An intron variant SNP on chromosome 5 at position 93,945,738 explained 7% of the variance for fat percentage, and 80% of the total variance explained by the multi-marker regression, confirming results from a study in the New Zealand dairy cattle population using different methodologies. Variants identified in this study are likely to provide improved predictive power for genomic evaluation of dairy cattle.