Skip to main content
ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #314777
Title: Genome-wide association study of fertility traits in dairy cattle using high-density single nucleotide polymorphism marker panels

Author
item PARKER GADDIS, KRISTEN - University Of Florida
item Cole, John

Submitted to: Journal of Dairy Science
Publication Type: Abstract Only
Publication Acceptance Date: 3/17/2015
Publication Date: 7/12/2015
Citation: Parker Gaddis, K.L., Cole, J.B. 2015. Genome-wide association study of fertility traits in dairy cattle using high-density single nucleotide polymorphism marker panels. Journal of Dairy Science. 98(Suppl. 2)/Journal of Animal Science 93(Suppl. 3):578(abstr. 538).

Interpretive Summary:

Technical Abstract: Unfavorable genetic correlations between production and fertility traits are well documented. Genetic selection for fertility traits is slow, however, due to low heritabilities. Identification of single nucleotide polymorphisms (SNP) involved in reproduction could improve reliability of genomic estimates for these low heritability traits. Additionally, high-density marker panels can increase the power of resultant GWAS by providing increased coverage and stronger linkage disequilibrium between markers and causal variants. The objective of this study was to identify SNP associated with three fertility traits in dairy cattle, daughter pregnancy rate (DPR), heifer conception rate (HCR), and cow conception rate (CCR), using high-density marker panels. Deregressed predicted transmitting abilities were available for 10,000 bulls sampled from the National Dairy Database that had high-density genotypes. Of those, 725 had been genotyped with the Illumina BovineHD Genotyping BeadChip. The remaining bulls had genotypes from various chip densities that were imputed up to the same level. After editing, 312,614 markers were included in the analyses. Univariate analyses were performed for DPR, HCR, and CCR using REMLF90 (version 1.79) with genomic options. postGSf90 (version 1.170) was used to calculate SNP effects and 10-SNP window variances. The largest proportion of variance explained for DPR (0.126%) was located on chromosome 6. Peaks were also identified on chromosomes 5, 18, and 28 associated with DPR. For HCR, the region explaining the largest proportion of variance (0.155%) was located on chromosome 1. Large peaks were also identified for HCR on chromosomes 6, 8, 14, and 17. The largest proportion of variance explained for CCR (0.181%) was located on chromosome 18. Large peaks associated with CCR were also identified on chromosomes 6, 15, and 19. Numerous markers and regions aligned with those previously identified. Significant SNPs could be used in genomic selection programs as well as in identification of genes and networks involved with fertility.