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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 #318541

Research Project: Improving Genetic Predictions in Dairy Animals Using Phenotypic and Genomic Information

Location: Animal Genomics and Improvement Laboratory

Title: Use of single nucleotide polymorphisms in candidate genes associated with daughter pregnancy rate for prediction of genetic merit for reproduction in Holstein cows

Author
item Ortega, M. Sofia - University Of Florida
item Denicol, Anna - University Of Florida
item Cole, John
item Null, Daniel
item Hansen, Peter - University Of Florida

Submitted to: Animal Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/24/2015
Publication Date: 6/1/2016
Citation: Ortega, M., Denicol, A.C., Cole, J.B., Null, D.J., Hansen, P.J. 2016. Use of single nucleotide polymorphisms in candidate genes associated with daughter pregnancy rate for prediction of genetic merit for reproduction in Holstein cows. Animal Genetics. 47(3):288–297.

Interpretive Summary: The effects of 69 DNA markers associated with fertility and production in previous studies were confirmed in a separate population of Holstein cows. Thirty of the 69 markers tested had statistically significant associations with three measures of fertility in cows. When those 39 markers were added to the set used to compute the national genetic evaluations, the reliability of the evaluations increased by 0.2%, which is similar to the gain from using a genotyping chip with 777,000 markers. These results can be used to increase the accuracy of fertility productions in 9,000,000 dairy cows in the US.

Technical Abstract: We evaluated 69 SNPs in genes previously related to fertility and production traits for relationship to daughter pregnancy rate (DPR), cow conception rate (CCR) and heifer conception rate (HCR) in a separate population of Holstein cows grouped according to their predicted transmitting ability for DPR: <= -1 (n=1287) and >= 1.5 (n=1036). Genotyping was by Sequenom MassARRAY®. There were a total of 39 SNPs associated with the three fertility traits. The SNPs that explained the greater proportion of the genetic variation for DPR were COQ9 (3.2%), EPAS1 (1.0%), CAST (1.0%), C7H19orf60 (1.0%), and MRPL48 (1.0%); for CCR were GOLGA4 (2.4%), COQ9 (1.8%), EPAS1 (1.1%) and MRPL48 (0.8%), and for HCR were HSD17B7 (1.0%), APB3B1 (0.8%), HSD17B12 (0.7%) and CACNA1D (0.6%). Inclusion of 39 SNPs previously associated to DPR in the genetic evaluation system increased the reliability of predicted transmitting ability (PTA) for DPR by 0.2%. Many of the genes represented by SNPs associated with fertility are involved in steroidogenesis or are regulated by steroids. A large proportion of SNPs previously associated with genetic merit for fertility in Holstein bulls maintained their association in a separate population of cows. The inclusion of these genes in genetic evaluation can improve reliabilities of genomic estimates for fertility.