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 #405469
Research Project: Increasing Accuracy of Genomic Prediction, Developing Algorithms, Selecting Markers, and Evaluating New Traits to Improve Dairy Cattle

Location: Animal Genomics and Improvement Laboratory

Title: A million-cow genome-wide association study of three fertility traits in U.S. Holstein cows

Author
item LIANG, ZUOXIANG - University Of Minnesota
item PRAKAPENKA, DZIANIS - University Of Minnesota
item Vanraden, Paul
item JIANG, JICAI - North Carolina State University
item MA, LI - University Of Maryland
item DA, YANG - University Of Minnesota

Submitted to: International Journal of Molecular Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/20/2023
Publication Date: 6/22/2023
Citation: Liang, Z., Prakapenka, D., Van Raden, P.M., Jiang, J., Ma, L., Da, Y. 2023. A million-cow genome-wide association study of three fertility traits in U.S. Holstein cows. International Journal of Molecular Sciences. 24(13):10496. https://doi.org/10.3390/ijms241310496.
DOI: https://doi.org/10.3390/ijms241310496

Interpretive Summary: Genetic progress is faster and predictions more accurate using carefully chosen genetic variants. Large sample sizes provide greater statistical power to detect true genetic effects assuming that many were not previously detected, to produce more reliable estimates of those effects, and to separate the likely true genetic effects from spurious associations. Most previous studies often used data for tens of thousands of bulls, but this study examined more than one million cows measured for three fertility traits. Most previous studies estimated only additive effects, but this study also detected dominant or recessive effects. The larger datasets and more complete genetic model detected more genetic variants useful for selection and mating programs for dairy cattle.

Technical Abstract: A genome-wide association study (GWAS) of daughter pregnancy rate (DPR), cow conception rate (CCR) and heifer conception rate (HCR) using 1,001,374-1,194,736 first lactation Holstein cows and 75,140-75,295 SNPs identified 7567, 3798 and 726 additive effects as well as 22, 27 and 25 dominance effects for DPR, CCR and HCR respectively with log10(1/p)>8. Most of these effects were new effects and some new effects were in or near genes known to affect reproduction in-cluding GNRHR, SHBG, ESR1, and a gene cluster of pregnancy associated glycoproteins. Con-firmed effects included those in or near the SLC4A4-GC-NPFFR2 and AFF1 regions of Cr06, and the KALRN region of Chr01. Eleven SNPs in the CEBPG-PEPD-CHST8 region of Chr18, the AFF1-KLHL8 region of Chr06 and the CCDC14-KALRN region of Chr01 with sharply negative allelic effects and dominance values for the recessive homozygous genotypes were recommended for heifer culling. Two SNPs in and near AGMO of Chr04 that were sharply negative for HCR and age at first calving but slightly positive for the yield traits could also be considered for heifer culling. Results from this study provided new evidence and understanding about the genetic variants and genome regions affecting the three fertility traits in U.S. Holstein cows.