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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Genetics and Animal Breeding » Research » Publications at this Location » Publication #309654
Title: Evaluation of single nucleotide polymorphisms in chromosomal regions impacting pregnancy status in cattle

Author
item PSAROS, KAYLA - North Carolina State University
item McDaneld, Tara
item Kuehn, Larry
item Snelling, Warren
item Keele, John

Submitted to: Journal of Animal Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/3/2015
Publication Date: 3/31/2015
Publication URL: http://handle.nal.usda.gov/10113/62247
Citation: Psaros, K.M., McDaneld, T.G., Kuehn, L.A., Snelling, W.M., Keele, J.W. 2015. Evaluation of single nucleotide polymorphisms in chromosomal regions impacting pregnancy status in cattle. Journal of Animal Science. 93(3):978-987. doi: 10.2527/jas2014-8509.

Interpretive Summary: Reproductive success is an important component of commercial beef cattle production, and identification of DNA markers with predictive merit for reproductive success would facilitate accurate prediction of mean daughter pregnancy rate, enabling effective selection of bulls to improve female fertility. A previous study initially identified single nucleotide polymorphisms (SNP) associated with beef cattle reproductive efficiency. For the current study, we expand upon this previous study and individually genotyped Bos indicus and Bos taurus cattle for 89 SNP previously associated with female pregnancy rate. From this research, regions on chromosomes 5 and 9 were significant (5% genome wide) through individual genotyping to harbor genetic variation affecting reproductive efficiency in interspecific crosses (Bos indicus and Bos taurus) of cattle. Additionally, a haplotype block (a form of DNA variation) with negative effects on reproduction was identified on chromosome 5 in cattle breeds with Bos indicus × Bos taurus composites.

Technical Abstract: Reproductive success is an important component of commercial beef cattle production, and identification of DNA markers with predictive merit for reproductive success would facilitate accurate prediction of mean daughter pregnancy rate, enabling effective selection of bulls to improve female fertility. A previous study initially identified SNP associated with beef cattle reproductive efficiency based on a genome-wide association analysis approach employing genotyping multiple-animal pools of DNA to increase the number of animals that could be genotyped with available resources. For the current study, we expand upon this previous study by individually genotyping cattle from the pooling study for 89 SNP that were previously associated with female pregnancy rate. The aims of the study were to confirm the results of the pooling study and more specifically identify modes of gene action and DNA variations such as haplotypes that would not be possible with pooled genotyping. Eighty-nine SNP selected from the pooling study were evaluated using the Sequenom MassARRAY system to individually genotype animals from populations evaluated in the previous pooling study, including both Bos indicus and Bos taurus breeds. From this research, regions on chromosomes 5 (26.3-48.1 Mb; UMD3.1 assembly) and 9 (37,436,575 bp; UMD3.1 assembly), first identified in the previous pooling study, were shown through individual genotyping to harbor genetic variation (P < 0.05 genome-wide significance) affecting reproductive efficiency in inter-specific crosses (Bos indicus and Bos taurus) of cattle. Each of these markers exhibited additive (vs. dominant) gene action. Additionally, a haplotype block harboring an allele of Bos indicus origin with negative effects on reproduction was identified on chromosome 5 in inter-specific composite breeds of Bos indicus × Bos taurus composites.